Yarrowia esterase/lipase promoter regions for gene expression in yeast

ABSTRACT

Promoter regions associated with the  Yarrowia lipolytica  esterase/lipase (EL1) gene are disclosed and have been found to be particularly effective for the expression of heterologous genes in yeast. These promoter regions will be useful for driving high-level expression of genes involved in the production of omega-3 and omega-6 fatty acids.

This application claims the benefit of U.S. Provisional Application No. 61/470,539, filed Apr. 1, 2011, which is incorporated herein by reference in its entirety.

FIELD OF THE INVENTION

This invention is in the field of biotechnology. More specifically, this invention pertains to esterase/lipase [“EL1”] promoter regions derived from Yarrowia lipolytica that are useful for gene expression in yeast.

BACKGROUND OF THE INVENTION

Oleaginous yeast are defined as those organisms that are naturally capable of oil synthesis and accumulation, wherein oil accumulation ranges from at least about 25% up to about 80% of the dry cell weight. The technology for growing oleaginous yeast with high oil content is well developed (for example, see EP 0 005 277B1; Ratledge, C., Prog. Ind. Microbiol., 16:119-206 (1982)). And, these organisms have been commercially used for a variety of purposes in the past.

Recently, the natural abilities of oleaginous yeast have been enhanced by advances in genetic engineering, resulting in organisms capable of producing polyunsaturated fatty acids [“PUFAs”], carotenoids, resveratrol and sterols. For example, significant efforts by Applicants' Assignee have demonstrated that Yarrowia lipolytica can be engineered for production of omega-3 and omega-6 fatty acids, by introducing and expressing genes encoding the omega-3/omega-6 biosynthetic pathway (U.S. Pat. No. 7,238,482; U.S. Pat. No. 7,465,564; U.S. Pat. No. 7,550,286; U.S. Pat. No. 7,588,931; and U.S. Pat. No. 7,932,077; U.S. Pat. Appl. Publ. Nos. 2009-0093543-A1 and 2010-0317072-A1).

Recombinant production of any heterologous protein is generally accomplished by constructing an expression cassette in which the DNA coding for the protein of interest is placed under the control of a promoter suitable for the host cell. The expression cassette is then introduced into the host cell (i.e., usually by plasmid-mediated transformation or targeted integration into the host genome) and production of the heterologous protein is achieved by culturing the transformed host cell under conditions necessary for the proper function of the promoter contained within the expression cassette. Thus, the development of new host cells (e.g., transformed yeast) for recombinant production of proteins generally requires the availability of promoters that are suitable for controlling the expression of a protein of interest in the host cell.

A variety of strong promoters have been isolated from Yarrowia lipolytica that are useful for heterologous gene expression in yeast, as shown in the Table below.

TABLE 1 Characterized Yarrowia lipolytica Promoters Promoter Name Native Gene Reference XPR2 alkaline extracellular protease U.S. Pat. No. 4,937,189; EP220864 TEF translation elongation factor EF1-α U.S. Pat. No. 6,265,185 (tef) GPD, GPM glyceraldehyde-3-phosphate- U.S. Pat. Nos. 7,259,255 dehydrogenase (gpd), and 7,459,546; U.S. Pat. phosphoglycerate mutase (gpm) Appl. Publ. No. 2011-0059496-A1 GPDIN glyceraldehyde-3-phosphate- U.S. Pat. No. 7,459,546 dehydrogenase (gpd) GPM/FBAIN chimeric phosphoglycerate mutase U.S. Pat. No. 7,202,356 (gpm)/fructose-bisphosphate aldolase (fba1) FBA, FBAIN, fructose-bisphosphate aldolase U.S. Pat. No. 7,202,356 FBAINm (fba1) GPAT glycerol-3-phosphate U.S. Pat. No. 7,264,949 O-acyltransferase (gpat) YAT1 ammonium transporter enzyme U.S. Pat. Appl. Publ. Nos. (yat1) 2006-0094102-A1 and 2010-0068789-A1 EXP1 export protein U.S. Pat. No. 7,932,077

Additionally, Juretzek et al. (Biotech. Bioprocess Eng., 5:320-326 (2000)) compares the glycerol-3-phosphate dehydrogenase [“G3P”], isocitrate lyase [“ICL1”], 3-oxo-acyl-CoA thiolase [“POT1”] and acyl-CoA oxidase [“POX1”, “POX2” and “POX5”] promoters with respect to their regulation and activities during growth on different carbon sources.

Despite the utility of these known promoters, however, there is a need for new improved yeast promoters for metabolic engineering of yeast (i.e., oleaginous and non-oleaginous) and for controlling the expression of heterologous genes in yeast. Furthermore, possession of a suite of promoters that can be regulated under a variety of natural growth and induction conditions in yeast will play an important role in industrial settings, wherein economical production of heterologous and/or homologous polypeptides in commercial quantities is desirable.

It is believed that promoter regions derived from the Yarrowia lipolytica gene encoding esterase/lipase [“EL1”] will be useful in expressing heterologous and/or homologous genes in transformed yeast, including Yarrowia.

SUMMARY OF THE INVENTION

In a first embodiment, the invention concerns a method for expressing a coding region of interest in a transformed yeast cell comprising:

-   -   a) providing a transformed yeast cell having a recombinant         construct, wherein the recombinant construct comprises:         -   (1) a promoter region of an EL1 Yarrowia gene; and         -   (2) a coding region of interest which is expressible in the             yeast cell;     -   wherein the promoter region is operably linked to the coding         region of interest; and     -   b) growing the transformed yeast cell of step (a) under         conditions whereby the recombinant construct of step (a) is         expressed.

In a second embodiment, the invention concerns a method for the production of an omega-3 fatty acid or omega-6 fatty acid comprising:

-   -   a) providing a transformed oleaginous yeast cell comprising a         recombinant construct, wherein the recombinant construct         comprises:         -   i) a promoter region of an EL1 Yarrowia gene; and         -   ii) a coding region encoding at least one omega-3 fatty acid             or omega-6 fatty acid biosynthetic pathway enzyme;         -   wherein the promoter region and the coding region are             operably linked;     -   b) growing the transformed oleaginous yeast of step (a) under         conditions whereby the at least one omega-3 fatty acid or         omega-6 fatty acid biosynthetic pathway enzyme is expressed and         the omega-3 fatty acid or the omega-6 fatty acid is produced;         and     -   c) optionally recovering the omega-3 fatty acid or the omega-6         fatty acid.

In another aspect, the promoter region of a Yarrowia gene may comprise a sequence selected from the group consisting of SEQ ID NO:30 and SEQ ID NO:32.

In yet another aspect, the promoter region of the EL1 Yarrowia gene further comprises an enhancer region set forth in SEQ ID NO:33, the enhancer region being operably linked to a functional yeast promoter.

In some embodiments, the promoter region of an EL1 Yarrowia gene may be as set forth in SEQ ID NO:6, wherein said promoter optionally comprises at least one modification selected from the group consisting of:

-   -   a) a deletion at the 5′-terminus of 1, 2, 3, 4, 5, 6, 7, 8, 9,         10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,         26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41,         42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57,         58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73,         74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89,         90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104,         105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117,         118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130,         131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143,         144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156,         157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169,         170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182,         183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195,         196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208,         209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221,         222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234,         235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247,         248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260,         261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273,         274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286,         287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299,         300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312,         313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325,         326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338,         339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351,         352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364,         365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377,         378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390,         391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403,         404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416,         417, 418, 419, 420, 421, 422, 423, 424, 425, 426, 427, 428, 429,         430, 431, 432, 433, 434, 435, 436, 437, 438, 439, 440, 441, 442,         443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453, 454, 455,         456, 457, 458, 459, 460, 461, 462, 463, 464, 465, 466, 467, 468,         469, 470, 471, 472, 473, 474, 475, 476, 477, 478, 479, 480, 481,         482, 483, 484, 485, 486, 487, 488, 489, 490, 491, 492, 493, 494,         495, 496, 497, 498, 499, 500, 501, 502, 503, 504, 505, 506, 507,         508, 509, 510, 511, 512, 513, 514, 515, 516, 517, 518, 519, 520,         521, 522, 523, 524, 525, 526, 527, 528, 529, 530, 531, 532, 533,         534, 535, 536, 537, 538, 539, 540, 541, 542, 543, 544, 545, 546,         547, 548, 549, 550, 551, 552, 553, 554, 555, 556, 557, 558, 559,         560, 561, 562, 563, 564, 565, 566, 567, 568, 569, 570, 571, 572,         573, 574, 575, 576, 577, 578, 579, 580, 581, 582, 583, 584, 585,         586, 587, 588, 589, 590, 591, 592, 593, 594, 595, or 596         consecutive nucleotides, wherein the first nucleotide deleted is         the guanine [‘G’] nucleotide at position 1 of SEQ ID NO:6;     -   b) substitution of an adenine [‘A’] nucleotide for the cytosine         [‘C’] nucleotide at position 856 of SEQ ID NO:6;     -   c) substitution of a thymine [‘T’] nucleotide or a guanine [‘G’]         nucleotide for the cytosine [‘C’] nucleotide at position +856 of         SEQ ID NO:6;     -   d) substitution of a cytosine [‘C’] nucleotide for the guanine         [‘G’] nucleotide at position 382 of SEQ ID NO:6;     -   e) substitution of an adenine [‘A’] nucleotide or a thymine         [‘T’] nucleotide for the guanine [‘G’] nucleotide at position         382 of SEQ ID NO:6;     -   f) insertion of a nucleotide sequence ‘TAAA’ between position         496 and position 497 of SEQ ID NO:6;     -   g) insertion of a nucleotide sequence ‘AC’ between position 596         and 597 of SEQ ID NO:6; and     -   h) any combination of part a), part b), part c), part d), part         e), part f), and part g) above.

More preferably, the promoter region of an EL1 Yarrowia gene may be as set forth in SEQ ID NO:29, wherein said promoter comprises at least one modification selected from the group consisting of:

-   -   a) a deletion at the 5′-terminus of 1, 2, 3, 4, 5, or 6,         consecutive nucleotides, wherein the first nucleotide deleted is         the thymine nucleotide [‘T’] at position 1 of SEQ ID NO:29;     -   b) a deletion at the 3′-terminus of 1, 2, 3, 4, 5, 6, 7, 8, 9,         10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,         26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41,         42, 43, 44, 45, 46, 47, or 48 consecutive nucleotides, wherein         the first nucleotide deleted is the cytosine [‘C’] at position         261 of SEQ ID NO:29; and     -   c) a deletion of part (a) in combination with a substitution of         a thymine [‘T’] nucleotide, adenine [‘A’] nucleotide or a         guanine [‘G’] nucleotide for the cytosine [‘C’] nucleotide at         position 260 of SEQ ID NO:29.

The promoter region of an EL1 Yarrowia gene may be selected from the group consisting of SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:16, SEQ ID NO:21, SEQ ID NO:25, SEQ ID NO:27, and SEQ ID NO:29.

In various embodiments of the methods of the invention, the transformed yeast cell is an oleaginous yeast. This oleaginous yeast may be a member of a genus selected from the group consisting of Yarrowia, Candida, Rhodotorula, Rhodosporidium, Cryptococcus, Trichosporon and Lipomyces.

Additionally, provided herein is an isolated nucleic acid molecule comprising a promoter region of an EL1 Yarrowia selected from the group consisting of:

-   -   (a) SEQ ID NO:8;     -   (b) SEQ ID NO:16;     -   (c) SEQ ID NO:21;     -   (d) SEQ ID NO:25;     -   (e) SEQ ID NO:27;     -   (f) SEQ ID NO:29;     -   (g) SEQ ID NO:6, wherein said promoter optionally comprises at         least one modification selected from the group consisting of:         -   (i) a deletion at the 5′-terminus of 1, 2, 3, 4, 5, 6, 7, 8,             9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,             24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38,             39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53,             54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68,             69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83,             84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98,             99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110,             111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122,             123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134,             135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146,             147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158,             159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170,             171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182,             183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194,             195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206,             207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218,             219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230,             231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242,             243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254,             255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266,             267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278,             279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290,             291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302,             303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314,             315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326,             327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338,             339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350,             351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362,             363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374,             375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, 386,             387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398,             399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410,             411, 412, 413, 414, 415, 416, 417, 418, 419, 420, 421, 422,             423, 424, 425, 426, 427, 428, 429, 430, 431, 432, 433, 434,             435, 436, 437, 438, 439, 440, 441, 442, 443, 444, 445, 446,             447, 448, 449, 450, 451, 452, 453, 454, 455, 456, 457, 458,             459, 460, 461, 462, 463, 464, 465, 466, 467, 468, 469, 470,             471, 472, 473, 474, 475, 476, 477, 478, 479, 480, 481, 482,             483, 484, 485, 486, 487, 488, 489, 490, 491, 492, 493, 494,             495, 496, 497, 498, 499, 500, 501, 502, 503, 504, 505, 506,             507, 508, 509, 510, 511, 512, 513, 514, 515, 516, 517, 518,             519, 520, 521, 522, 523, 524, 525, 526, 527, 528, 529, 530,             531, 532, 533, 534, 535, 536, 537, 538, 539, 540, 541, 542,             543, 544, 545, 546, 547, 548, 549, 550, 551, 552, 553, 554,             555, 556, 557, 558, 559, 560, 561, 562, 563, 564, 565, 566,             567, 568, 569, 570, 571, 572, 573, 574, 575, 576, 577, 578,             579, 580, 581, 582, 583, 584, 585, 586, 587, 588, 589, 590,             591, 592, 593, 594, 595, or 596 consecutive nucleotides,             wherein the first nucleotide deleted is the guanine [‘G’]             nucleotide at position 1 of SEQ ID NO:6;         -   (ii) substitution of an adenine [‘A’] nucleotide for the             cytosine [‘C’] nucleotide at position 856 of SEQ ID NO:6;         -   (iii) substitution of a thymine [‘T’] nucleotide or a             guanine [‘G’] nucleotide for the cytosine [‘C’] nucleotide             at position 856 of SEQ ID NO:6;         -   (iv) substitution of a cytosine [‘C’] nucleotide for the             guanine [‘G’] nucleotide at position 382 of SEQ ID NO:6;         -   (v) substitution of an adenine [‘A’] nucleotide or a thymine             [‘T’] nucleotide for the guanine [‘G’] nucleotide at             position 382 of SEQ ID NO:6;         -   (vi) insertion of a nucleotide sequence ‘TAAA’ between             position 496 and position 497 of SEQ ID NO:6;         -   (vii) insertion of a nucleotide sequence ‘AC’ between             position 596 and 597 of SEQ ID NO:6; and         -   (viii) any combination of part (i), part (ii), part (iii),             part (iv), part (v), part (vi), and part (vii) above; and     -   (h) a promoter region comprising SEQ ID NO:32.

Also provided herein is an isolated nucleic acid molecule comprising a promoter region of an EL1 Yarrowia gene, wherein the promoter region of the EL1 Yarrowia gene further comprises an enhancer region set forth in SEQ ID NO:33, the enhancer region being operably linked to a functional yeast promoter.

BRIEF DESCRIPTION OF THE DRAWINGS AND SEQUENCE DESCRIPTIONS

FIG. 1 graphically represents the relationship between SEQ ID NOs:2, 6, 16, 27, 29, and 30, each of which relates to promoter regions derived from the 5′ upstream region of the esterase/lipase [“EL1”] gene in Yarrowia lipolytica.

FIGS. 2A, 2B, 2C, 2D, and 2E (which should be viewed together as FIG. 2) provide an alignment of:

-   -   (a) the Y. lipolytica EL1F (SEQ ID NO:2) promoter region, which         is the 1000 bp 5′ upstream sequence (i.e., the −1000 to −1         region) of the esterase/lipase [“EL1”] gene in Y. lipolytica,         wherein the nucleotide ‘A’ of the EL1 translation initiation         codon ‘ATG’ was designated as +1 (note that the ATG codon is not         shown in the figure);     -   (b) the 857 bp EL1L (SEQ ID NO:6) promoter region;     -   (c) the 720 bp EL1LM-P2P1 (SEQ ID NO:21) promoter region;     -   (d) the 718 bp EL1LM-P2P2 (SEQ ID NO:25) promoter region;     -   (e) the 716 bp EL1LM-P2 (SEQ ID NO:16) promoter region;     -   (f) the 361 bp EL1-P4 (SEQ ID NO:27) promoter region;     -   (g) the 261 bp EL1-P5 (SEQ ID NO:29) promoter region; and     -   (h) the 207 bp EL1 minimal (Core) (SEQ ID NO:30) promoter         region.         Base pair differences are highlighted with an arrow and box.

FIG. 3 illustrates the omega-3/omega-6 fatty acid biosynthetic pathway.

FIG. 4 provides plasmid maps for the following: (A) pDMW212 and (B) pEL1GUS.

FIG. 5 is an image of cell cultures comparing the promoter activity of 857 bp EL1LM (SEQ ID NO:8) and FBA in Yarrowia lipolytica as determined by histochemical staining.

The invention can be more fully understood from the following detailed description and the accompanying sequence descriptions, which form a part of this application.

SEQ ID NOs:1-34 are promoters, ORFs encoding genes (or portions thereof), primers, or plasmids, as identified in Table 2.

TABLE 2 Summary of Nucleic Acid SEQ ID Numbers Nucleic acid Description SEQ ID NO. Yarrowia EL1 gene (“YALI0E19899g”)  1 (2359 bp) 1000 bp EL1F Yarrowia promoter region  2 (1000 bp) Primer Y1210  3 (34 bp) Primer Y1211  4 (38 bp) Plasmid pT-EL1  5 (4824 bp) 857 bp EL1L Yarrowia promoter region  6 (857 bp) Plasmid pT-EL1-(S)  7 (4824 bp) 857 bp EL1LM Yarrowia promoter region  8 (857 bp) Primer Y1212  9 (35 bp) Primer Y1213 10 (35 bp) Plasmid pT-EL1-(S)P2 11 (4828 bp) Primer Y1242 12 (38 bp) Primer Y1243 13 (38 bp) Plasmid pDMW212 14 (9348 bp) Plasmid pEL1GUS 15 (9392 bp) 716 bp EL1LM-P2 Yarrowia promoter region 16 (716 bp) Plasmid pEL1GUS2 17 (9231 bp) Primer Y1254 18 (39 bp) Primer Y1255 19 (39 bp) Plasmid pEL1GUS2-P1 20 (9226 bp) 720 bp EL1LM-P2P1 Yarrowia promoter region 21 (720 bp) Primer Y1256 22 (36 bp) Primer Y1257 23 (36 bp) Plasmid pEL1GUS2-P2 24 (9224 bp) 718 bp EL1LM-P2P2 Yarrowia promoter region 25 (718 bp) Plasmid pEL1GUS2-P4 26 (8667 bp) 361 bp EL1-P4 Yarrowia promoter region 27 (361 bp) Plasmid pEL1GUS2-P5 28 (8768 bp) 261 bp EL1-P5 Yarrowia promoter region 29 (261 bp) 207 bp EL1 Minimal promoter 30 (207 bp) 861 bp EL1LM + Pme Yarrowia promoter region 31 (861 bp) 255 bp EL1 Minimal promoter region 32 (255 bp) 357 bp EL1 Yarrowia enhancer region 33 (357 bp) Consensus sequence [A(A_(rich))₅NYA(A/T)NN(A_(rich))₆] 34 (18 bp) located in promoter sequences of S. cerevisiae genes

DETAILED DESCRIPTION OF THE INVENTION

All patents, patent applications, and publications cited herein are hereby incorporated by reference in their entirety.

In this disclosure, a number of terms and abbreviations are used. The following definitions are provided.

“Open reading frame” is abbreviated “ORF”.

“Polymerase chain reaction” is abbreviated “PCR”.

“American Type Culture Collection” is abbreviated “ATCC”.

“Polyunsaturated fatty acid(s)” is abbreviated “PUFA(s)”.

“Triacylglycerols” are abbreviated “TAGs”.

The term “yeast” refers to a phylogenetically diverse grouping of single-celled fungi. Yeast do not form a specific taxonomic or phylogenetic grouping, but instead comprise a diverse assemblage of unicellular organisms that occur in the Ascomycotina and Basidiomycotina. Collectively, about 100 genera of yeast have been identified, comprising approximately 1,500 species (Kurtzman and Fell, Yeast Systematics And Phylogeny: Implications Of Molecular Identification Methods For Studies In Ecology. In C. A. Rosa and G. Peter, eds., The Yeast Handbook. Germany: Springer-Verlag Berlin Herdelberg, 2006). Yeast reproduce principally by budding (or fission) and derive energy from fermentation, via conversion of carbohydrates to ethanol and carbon dioxide. Examples of some yeast genera include, but are not limited to: Agaricostilbum, Ambrosiozyma, Arthroascus, Arxula, Ashbya, Babjevia, Bensingtonia, Botryozyma, Brettanomyces, Bullera, Candida, Clavispora, Cryptococcus, Cystofilobasidium, Debaryomyces, Dekkera, Dipodascus, Endomyces, Endomycopsella, Erythrobasidium, Fellomyces, Filobasidium, Galactomyces, Geotrichum, Guilliermondella, Hansenula, Hanseniaspora, Kazachstania, Kloeckera, Kluyveromyces, Kockovaella, Kodamaea, Komagataella, Kondoa, Lachancea, Leucosporidium, Leucosporidiella, Lipomyces, Lodderomyces, Issatchenkia, Magnusiomyces, Mastigobasidium, Metschnikowia, Monosporella, Myxozyma, Nadsonia, Nematospora, Oosporidium, Pachysolen, Pichia, Phaffia, Pseudozyma, Reniforma, Rhodosporidium, Rhodotorula, Saccharomyces, Saccharomycodes, Saccharomycopsis, Saturnispora, Schizoblastosporion, Schizosaccharomyces, Sirobasidium, Smithiozyma, Sporobolomyces, Sporopachydermia, Starmerella, Sympodiomycopsis, Sympodiomyces, Torulaspora, Tremella, Trichosporon, Trichosporiella, Trigonopsis, Udeniomyces, Wickerhamomyces, Williopsis, Xanthophyllomyces, Yarrowia, Zygosaccharomyces, Zygotorulaspora, Zymoxenogloea and Zygozyma.

The term “oleaginous” refers to those organisms that tend to store their energy source in the form of oil (Weete, In: Fungal Lipid Biochemistry, 2^(nd) Ed., Plenum, 1980). Generally, the cellular oil content of oleaginous microorganisms follows a sigmoid curve, wherein the concentration of lipid increases until it reaches a maximum at the late logarithmic or early stationary growth phase and then gradually decreases during the late stationary and death phases (Yongmanitchai and Ward, Appl. Environ. Microbiol., 57:419-25 (1991)). It is common for oleaginous microorganisms to accumulate in excess of about 25% of their dry cell weight as oil.

The term “oleaginous yeast” refers to those microorganisms classified as yeasts that can make oil. Examples of oleaginous yeast include, but are not limited to, the following genera: Yarrowia, Candida, Rhodotorula, Rhodosporidium, Cryptococcus, Trichosporon and Lipomyces. Alternatively, organisms classified as yeasts that are genetically modified to become oleaginous such that they can produce more than 25% of their dry cell weight as oil are also “oleaginous”, e.g., yeast such as Saccharomyces cerevisiae (Intl Appl. Pub. No. WO 2006/102342).

The term “fermentable carbon source” will refer to a carbon source that a microorganism will metabolize to derive energy. Typical carbon sources for use in the methods herein include, but are not limited to: monosaccharides, disaccharides, oligosaccharides, polysaccharides, alkanes, fatty acids, esters of fatty acids, glycerol, monoglycerides, diglycerides, triglycerides, carbon dioxide, methanol, formaldehyde, formate and carbon-containing amines. Most preferred is glucose, sucrose, invert sucrose, fructose, glycerol and/or fatty acids containing between 10-22 carbons. The term “invert sucrose” (or “invert sugar”) refers to a mixture comprising equal parts of fructose and glucose resulting from the hydrolysis of sucrose. Invert sucrose may be a mixture comprising 25 to 50% glucose and 25 to 50% fructose. Invert sucrose may also comprise sucrose, the amount of which depends on the degree of hydrolysis.

The term “EL1” refers to a hypothetical protein weakly homologous to esterase/lipase (“YALI0E19899g”, Dujon, B. et al., Nature, 430(6995):35-44 (2004)) encoded by the EL1 gene and its transcription was increased in Yarrowia strains with their native snf1 gene knocked-out (U.S. Pat. Appl. Publ. No. 2010-0062502-A1). The EL1 enzyme catalyzes the hydrolysis of fatty acid ester bonds in triacylglycerols to release free fatty acids.

An “EL1 Yarrowia gene” refers to a gene encoding EL1 from a yeast of the genus Yarrowia. For example, a 2,239 bp DNA sequence (“YALI0E19899g”) that encodes a hypothetical protein weakly homologous to Esterase/Lipase is provided as SEQ ID NO:1 (Dujon, B. et al., Nature, 430(6995):35-44 (2004)).

The term “promoter region of an EL1 Yarrowia gene” or “Yarrowia EL1 promoter region” refers to the 5′ upstream untranslated region in front of the ‘ATG’ translation initiation codon of a Yarrowia EL1 gene, or sequences derived therefrom, and that is necessary for expression. Thus, it is believed that promoter regions of an EL1 Yarrowia gene will comprise a portion of the ˜1000 bp 5′ upstream of an EL1 Yarrowia gene. The sequence of the Yarrowia EL1 promoter region may correspond exactly to native sequence upstream of the EL1 Yarrowia gene (i.e., a “wildtype” or “native” Yarrowia EL1 promoter); alternately, the sequence of the Yarrowia EL1 promoter region may be “modified” or “mutated”, thereby comprising various substitutions, deletions, and/or insertions of one or more nucleotides relative to a wildtype or native Yarrowia EL1 promoter. These modifications can result in a modified Yarrowia EL1 promoter having increased, decreased or equivalent promoter activity, when compared to the promoter activity of the corresponding wildtype or native Yarrowia EL1 promoter. The term “mutant promoter” or “modified promoter” will encompass natural variants and in vitro generated variants obtained using methods well known in the art (e.g., classical mutagenesis, site-directed mutagenesis and “DNA shuffling”).

Described herein is a wildtype Yarrowia EL1 promoter region (SEQ ID NO:2) comprising the −1000 to −1 upstream region of the EL1 gene (SEQ ID NO:1) based on nucleotide numbering such that the ‘A’ position of the ‘ATG’ translation initiation codon is designated as +1. The ATG translation initiation codon is located at nucleotide positions 1001-1003 in SEQ ID NO:1. Alternately, and yet by no means limiting in nature, a wildtype Yarrowia EL1 promoter region may comprise the −857 to −1 region of SEQ ID NO:1, the −720 to −1 region of SEQ ID NO:1, the −718 to −1 region of SEQ ID NO:1, the −716 to −1 region of SEQ ID NO:1, the −361 to −1 region of SEQ ID NO:1, the −261 to −1 region of SEQ ID NO:1, the −255 to −1 region of SEQ ID NO:1; or the −255 to −48 region of SEQ ID NO:1 (where the “−1” position in SEQ ID NO:1 is the nucleotide that is 5′-adjacent to the ATG translation initiation codon). Similarly, a modified Yarrowia EL1 promoter region may comprise the promoter region of a EL1 Yarrowia gene as set forth in SEQ ID NO:6, wherein said promoter optionally comprises at least one modification selected from the group consisting of:

-   -   a) a deletion at the 5′-terminus of 1, 2, 3, 4, 5, 6, 7, 8, 9,         10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,         26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41,         42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57,         58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73,         74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89,         90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104,         105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117,         118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130,         131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143,         144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156,         157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169,         170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182,         183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195,         196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208,         209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221,         222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234,         235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247,         248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260,         261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273,         274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286,         287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299,         300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312,         313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325,         326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338,         339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351,         352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364,         365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377,         378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390,         391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403,         404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416,         417, 418, 419, 420, 421, 422, 423, 424, 425, 426, 427, 428, 429,         430, 431, 432, 433, 434, 435, 436, 437, 438, 439, 440, 441, 442,         443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453, 454, 455,         456, 457, 458, 459, 460, 461, 462, 463, 464, 465, 466, 467, 468,         469, 470, 471, 472, 473, 474, 475, 476, 477, 478, 479, 480, 481,         482, 483, 484, 485, 486, 487, 488, 489, 490, 491, 492, 493, 494,         495, 496, 497, 498, 499, 500, 501, 502, 503, 504, 505, 506, 507,         508, 509, 510, 511, 512, 513, 514, 515, 516, 517, 518, 519, 520,         521, 522, 523, 524, 525, 526, 527, 528, 529, 530, 531, 532, 533,         534, 535, 536, 537, 538, 539, 540, 541, 542, 543, 544, 545, 546,         547, 548, 549, 550, 551, 552, 553, 554, 555, 556, 557, 558, 559,         560, 561, 562, 563, 564, 565, 566, 567, 568, 569, 570, 571, 572,         573, 574, 575, 576, 577, 578, 579, 580, 581, 582, 583, 584, 585,         586, 587, 588, 589, 590, 591, 592, 593, 594, 595, or 596         consecutive nucleotides, wherein the first nucleotide deleted is         the guanine [‘G’] nucleotide at position 1 of SEQ ID NO:6;     -   b) substitution of an adenine [‘A’] nucleotide for the cytosine         [‘C’] nucleotide at position 856 of SEQ ID NO:6;     -   c) substitution of a thymine [‘T’] nucleotide or a guanine [‘G’]         nucleotide for the cytosine [‘C’] nucleotide at position 856 of         SEQ ID NO:6;     -   d) substitution of a cytosine [‘C’] nucleotide for the guanine         [‘G’] nucleotide at position 382 of SEQ ID NO:6;     -   e) substitution of an adenine [‘A’] nucleotide or a thymine         [‘T’] nucleotide for the guanine [‘G’] nucleotide at position         382 of SEQ ID NO:6;     -   f) insertion of a nucleotide sequence ‘TAAA’ between position         496 and position 497 of SEQ ID NO:6;     -   g) insertion of a nucleotide sequence ‘AC’ between position 596         and 597 of SEQ ID NO:6; and h) any combination of part a), part         b), part c), part d), part e), part f), and part g) above.         These examples are not intended to be limiting in nature and         will be elaborated below. FIG. 1 graphically illustrates various         Yarrowia EL1 promoter regions (i.e., SEQ ID NO:6 [857 bp EL1L],         SEQ ID NO:8 [857 bp EL1LM]; SEQ ID NO:16 [716 bp EL1LM-P2], SEQ         ID NO:27 [361 bp EL1-P4], SEQ ID NO:29 [261 bp EL1-P5], and SEQ         ID NO:30 [207 bp minimal/core EL1 promoter]), with the 1000 bp         5′ upstream region (SEQ ID NO:2) of the EL1 initiation codon of         the Yarrowia EL1 gene as a reference.

The term “promoter activity” will refer to an assessment of the transcriptional efficiency of a promoter. This may, for instance, be determined directly by measurement of the amount of mRNA transcription from the promoter (e.g., by quantitative PCR or Northern blotting or primer extension methods) or indirectly by measuring the amount of gene product expressed from the promoter.

The terms “polynucleotide”, “polynucleotide sequence”, “nucleic acid sequence”, “nucleic acid fragment” and “isolated nucleic acid fragment” are used interchangeably herein. These terms encompass nucleotide sequences and the like. A polynucleotide may be a polymer of RNA or DNA that is single- or double-stranded that optionally contains synthetic, non-natural or altered nucleotide bases. A polynucleotide in the form of a polymer of DNA may be comprised of one or more segments of cDNA, genomic DNA, synthetic DNA, or mixtures thereof. Nucleotides (usually found in their 5′-monophosphate form) are referred to by a single letter designation as follows: “A” for adenylate or deoxyadenylate (for RNA or DNA, respectively), “C” for cytidylate or deoxycytidylate, “G” for guanylate or deoxyguanylate, “U” for uridylate, “T” for deoxythymidylate, “R” for purines (A or G), “Y” for pyrimidines (C or T), “K” for G or T, “H” for A or C or T, “I” for inosine, and “N” for any nucleotide.

A “substantial portion” of an amino acid sequence or nucleotide sequence is that portion comprising enough of the amino acid sequence of a polypeptide or the nucleotide sequence of a gene to putatively identify that polypeptide or gene, either by manual evaluation of the sequence by one skilled in the art, or by computer-automated sequence comparison and identification using algorithms such as BLAST (Basic Local Alignment Search Tool; Altschul, S. F., et al., J. Mol. Biol. 215:403-410 (1993)). In general, a sequence of ten or more contiguous amino acids or thirty or more nucleotides is necessary in order to identify putatively a polypeptide or nucleic acid sequence as homologous to a known protein or gene. Moreover, with respect to nucleotide sequences, gene-specific oligonucleotide probes comprising 20-30 contiguous nucleotides may be used in sequence-dependent methods of gene identification (e.g., Southern hybridization) and isolation (e.g., in situ hybridization of bacterial colonies or bacteriophage plaques). In addition, short oligonucleotides of 12-15 bases may be used as amplification primers in PCR in order to obtain a particular nucleic acid molecule comprising the primers. Accordingly, a “substantial portion” of a nucleotide sequence comprises enough of the sequence to specifically identify and/or isolate a nucleic acid molecule comprising the sequence.

Disclosed herein are partial or complete nucleotide sequences containing one or more particular yeast promoters. The skilled artisan, having the benefit of the sequences as reported herein, may now use all or a substantial portion of the disclosed sequences for purposes known to those skilled in this art. Accordingly, the complete sequences as reported in the accompanying Sequence Listing, as well as substantial portions of those sequences as defined above, are encompassed in the present disclosure.

The term “complementary” is used to describe the relationship between nucleotide bases that are capable of hybridizing to one another. For example, with respect to DNA, adenosine is complementary to thymine and cytosine is complementary to guanine. Accordingly, isolated nucleic acid fragments that are complementary to the complete sequences as reported in the accompanying Sequence Listing, as well as those substantially similar nucleic acid sequences, are encompassed in the present disclosure.

The terms “homology”, “homologous”, “substantially similar” and “corresponding substantially” are used interchangeably herein. They refer to nucleic acid fragments wherein changes in one or more nucleotide bases do not affect the ability of the nucleic acid fragment to mediate gene expression or produce a certain phenotype. These terms also refer to modifications of the nucleic acid fragments of the instant invention such as deletion or insertion of one or more nucleotides that do not substantially alter the functional properties of the resulting nucleic acid fragment relative to the initial, unmodified fragment. It is therefore understood, as those skilled in the art will appreciate, that the disclosure herein encompasses more than the specific exemplary sequences.

“Sequence identity” or “identity” in the context of nucleic acid or polypeptide sequences refers to the nucleic acid bases or amino acid residues in two sequences that are the same when aligned for maximum correspondence over a specified comparison window.

Thus, “percentage of sequence identity” or “percent identity” refers to the value determined by comparing two optimally aligned sequences over a comparison window, wherein the portion of the polynucleotide or polypeptide sequence in the comparison window may comprise additions or deletions (i.e., gaps) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison and multiplying the results by 100 to yield the percentage of sequence identity.

Methods to determine “percent identity” and “percent similarity” are codified in publicly available computer programs. Percent identity and percent similarity can be readily calculated by known methods, including but not limited to those described in: 1) Computational Molecular Biology (Lesk, A. M., Ed.) Oxford University: NY (1988); 2) Biocomputing: Informatics and Genome Projects (Smith, D. W., Ed.) Academic: NY (1993); 3) Computer Analysis of Sequence Data, Part I (Griffin, A. M., and Griffin, H. G., Eds.) Humania: NJ (1994); 4) Sequence Analysis in Molecular Biology (von Heinje, G., Ed.) Academic (1987); and, 5) Sequence Analysis Primer (Gribskov, M. and Devereux, J., Eds.) Stockton: NY (1991).

Sequence alignments and percent identity or similarity calculations may be determined using a variety of comparison methods designed to detect homologous sequences including, but not limited to, the MegAlign™ program of the LASERGENE bioinformatics computing suite (DNASTAR Inc., Madison, Wis.). Multiple alignment of the sequences is performed using the “Clustal method of alignment” which encompasses several varieties of the algorithm including the “Clustal V method of alignment” and the “Clustal W method of alignment” (described by Higgins and Sharp, CABIOS, 5:151-153 (1989); Higgins, D. G. et al., Comput. Appl. Biosci., 8:189-191 (1992)) and found in the MegAlign™ (version 8.0.2) program of the LASERGENE bioinformatics computing suite (DNASTAR Inc.). After alignment of the sequences using either Clustal program, it is possible to obtain a “percent identity” by viewing the “sequence distances” table in the program.

For multiple alignments using the Clustal V method of alignment, the default values correspond to GAP PENALTY=10 and GAP LENGTH PENALTY=10. Default parameters for pairwise alignments and calculation of percent identity of protein sequences using the Clustal V method are KTUPLE=1, GAP PENALTY=3, WINDOW=5 and DIAGONALS SAVED=5. For nucleic acids these parameters are KTUPLE=2, GAP PENALTY=5, WINDOW=4 and DIAGONALS SAVED=4.

Default parameters for multiple alignment using the Clustal W method of alignment correspond to GAP PENALTY=10, GAP LENGTH PENALTY=0.2, Delay Divergent Seqs (%)=30, DNA Transition Weight=0.5, Protein Weight Matrix=Gonnet Series, DNA Weight Matrix=IUB.

The “BLASTN method of alignment” is an algorithm provided by the National Center for Biotechnology Information [“NCBI”] to compare nucleotide sequences using default parameters, while the “BLASTP method of alignment” is an algorithm provided by the NCBI to compare protein sequences using default parameters.

It is well understood by one skilled in the art that many levels of sequence identity are useful in identifying polypeptides from other species, wherein such polypeptides have the same or similar function or activity. Likewise, suitable promoter regions (isolated polynucleotides of the present invention) are at least about 70-85% identical, and more preferably at least about 85-95% identical to the nucleotide sequences reported herein. Although preferred ranges are described above, useful examples of percent identities include any integer percentage from 70% to 100%, such as 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99%. Suitable Yarrowia EL1 promoter regions not only have the above homologies but typically are at least 50 nucleotides in length, more preferably at least 100 nucleotides in length, more preferably at least 250 nucleotides in length, and more preferably at least 500 nucleotides in length.

“Codon degeneracy” refers to the nature in the genetic code permitting variation of the nucleotide sequence without affecting the amino acid sequence of an encoded polypeptide. The skilled artisan is well aware of the “codon-bias” exhibited by a specific host cell in usage of nucleotide codons to specify a given amino acid. Therefore, when synthesizing a gene for improved expression in a host cell, it is desirable to design the gene such that its frequency of codon usage approaches the frequency of preferred codon usage of the host cell.

“Synthetic genes” can be assembled from oligonucleotide building blocks that are chemically synthesized using procedures known to those skilled in the art. These oligonucleotide building blocks are annealed and then ligated to form gene segments that are then enzymatically assembled to construct the entire gene. Accordingly, the genes can be tailored for optimal gene expression based on optimization of nucleotide sequence to reflect the codon bias of the host cell. The skilled artisan appreciates the likelihood of successful gene expression if codon usage is biased towards those codons favored by the host. Determination of preferred codons can be based on a survey of genes derived from the host cell, where sequence information is available. For example, the codon usage profile for Yarrowia lipolytica is provided in U.S. Pat. No. 7,125,672.

“Gene” refers to a nucleic acid fragment that expresses a specific protein, and that may refer to the coding region alone or may include regulatory sequences preceding (5′ non-coding sequences) and following (3′ non-coding sequences) the coding sequence. “Native gene” refers to a gene as found in nature with its own regulatory sequences. “Chimeric gene” refers to any gene that is not a native gene, comprising regulatory and coding sequences that are not found together in nature. Accordingly, a chimeric gene may comprise regulatory sequences and coding sequences that are derived from different sources, or regulatory sequences and coding sequences derived from the same source, but arranged in a manner different than that found in nature. Chimeric genes herein will typically comprise a promoter region of an EL1 Yarrowia gene operably linked to a coding region of interest. “Endogenous gene” refers to a native gene in its natural location in the genome of an organism. A “foreign” gene refers to a gene that is introduced into the host organism by gene transfer. Foreign genes can comprise native genes inserted into a non-native organism, native genes introduced into a new location within the native host, or chimeric genes. A “transgene” is a gene that has been introduced into the genome by a transformation procedure. A “codon-optimized gene” is a gene having its frequency of codon usage designed to mimic the frequency of preferred codon usage of the host cell.

“Coding sequence” refers to a DNA sequence which codes for a specific amino acid sequence. The terms “coding sequence” and “coding region” are used interchangeably herein. A “coding region of interest” is a coding region which is desired to be expressed. Such coding regions are discussed more fully hereinbelow. “Regulatory sequences” refer to nucleotide sequences located upstream (5′ non-coding sequences), within, or downstream (3′ non-coding sequences) of a coding sequence, and which influence the transcription, RNA processing or stability, or translation of the associated coding sequence. Regulatory sequences may include, but are not limited to: promoters, enhancers, silencers, 5′ untranslated leader sequence (e.g., between the transcription start site and translation initiation codon), introns, polyadenylation recognition sequences, RNA processing sites, effector binding sites and stem-loop structures.

“Promoter” refers to a DNA sequence that facilitates transcription of a coding sequence, thereby enabling gene expression. In general, a promoter is typically located on the same strand and upstream of the coding sequence (i.e., 5′ of the coding sequence). Promoters may be derived in their entirety from a native gene, or be composed of different elements derived from different promoters found in nature, or even comprise synthetic DNA segments. It is understood by those skilled in the art that different promoters may direct the expression of a gene in different tissues or cell types, or at different stages of development, or in response to different environmental or physiological conditions. Promoters that cause a gene to be expressed at almost all stages of development are commonly referred to as “constitutive promoters”. It is further recognized that since in most cases the exact boundaries of regulatory sequences (especially at their 5′ end) have not been completely defined, DNA fragments of some variation may have identical promoter activity.

“Minimal promoter” refers to the minimal length of DNA sequence that is necessary to initiate basal level transcription of an operably linked coding sequence. The “minimal promoter” usually does not include the untranslated region located between transcription start site and translation start site. Although promoters often interact with the TATA binding protein [“TBP”] to create a transcription initiation complex from which RNA polymerase II transcribes the DNA coding sequence, only some promoters contain a TATA box to which TBP binds directly. In yeast, the TATA-box is usually located about 20 to 130 bp upstream of the transcription start site. For those TATA-less promoters, it is thought that transcription factor TFIID coordinates delivery of TBP and functions largely to stabilize TBP binding in lieu of a TATA box (Basehoar et al., Cell, 116:699-709 (2004)). Some TATA-less promoters contain an “initiator” element [A(A_(rich))₅NYA(A/T)NN(A_(rich))₆ (SEQ ID NO:34), Zhang, Z., and Dietrich, F. S., Nucleic Acids Res., 33:2838-2851 (2005), incorporated herein by reference] located around the transcription start site, which can direct basal level transcription.

Thus, the minimal promoter region for the EL1 TATA-less promoters is herein defined as the −255 to −48 region upstream of the EL1 gene (i.e., as set forth in SEQ ID NO:30), which contains initiator elements sufficient to initiate basal level transcription of an operably linked coding sequence. Alternately, the −255 to −1 region will also be a useful minimal promoter region (SEQ ID NO:32).

The terms “3′ non-coding sequences”, “transcription terminator” and “termination sequences” refer to DNA sequences located downstream of a coding sequence. This includes polyadenylation recognition sequences and other sequences encoding regulatory signals capable of affecting mRNA processing or gene expression. The polyadenylation signal is usually characterized by affecting the addition of polyadenylic acid tracts to the 3′ end of the mRNA precursor. The 3′ region can influence the transcription, RNA processing or stability, or translation of the associated coding sequence.

The term “enhancer” refers to a cis-regulatory sequence that can elevate levels of transcription from an adjacent eukaryotic promoter, thereby increasing transcription of the gene. Enhancers can act on promoters over many kilobases of DNA and can be 5′ or 3′ to the promoter they regulate. Enhancers can also be located within introns (Giacopelli F. et al., Gene Expr., 11:95-104 (2003)).

“RNA transcript” refers to the product resulting from RNA polymerase-catalyzed transcription of a DNA sequence. When the RNA transcript is a perfect complementary copy of the DNA sequence, it is referred to as the primary transcript or it may be a RNA sequence derived from post-transcriptional processing of the primary transcript and is referred to as the mature RNA. “Messenger RNA” or “mRNA” refers to the RNA that is without introns and that can be translated into protein by the cell. “cDNA” refers to a double-stranded DNA that is complementary to, and derived from, mRNA. “Sense” RNA refers to RNA transcript that includes the mRNA and so can be translated into protein by the cell. “Antisense RNA” refers to an RNA transcript that is complementary to all or part of a target primary transcript or mRNA, and that blocks the expression of a target gene (U.S. Pat. No. 5,107,065).

The term “operably linked” refers to the association of nucleic acid sequences on a single nucleic acid molecule so that the function of one is affected by the other. For example, a promoter is operably linked with a coding sequence when it is capable of affecting the expression of that coding sequence, i.e., the coding sequence is under the transcriptional control of the promoter. Coding sequences can be operably linked to regulatory sequences in sense or antisense orientation.

The term “recombinant” refers to an artificial combination of two otherwise separated segments of sequence, e.g., by chemical synthesis or by the manipulation of isolated segments of nucleic acids by genetic engineering techniques.

The term “expression”, as used herein, refers to the transcription and stable accumulation of sense (mRNA) or antisense RNA. Expression may also refer to translation of mRNA into a protein (either precursor or mature).

“Transformation” refers to the transfer of a nucleic acid molecule into a host organism, resulting in genetically stable inheritance. The nucleic acid molecule may be a plasmid that replicates autonomously, for example, or, it may integrate into the genome of the host organism. Host organisms containing the transformed nucleic acid fragments are referred to as “transgenic” or “recombinant” or “transformed” or “transformant” organisms.

The terms “plasmid” and “vector” refer to an extra chromosomal element often carrying genes that are not part of the central metabolism of the cell, and usually in the form of circular double-stranded DNA fragments. Such elements may be autonomously replicating sequences, genome integrating sequences, phage or nucleotide sequences, linear or circular, of a single- or double-stranded DNA or RNA, derived from any source, in which a number of nucleotide sequences have been joined or recombined into a unique construction which is capable of introducing an expression cassette(s) into a cell.

The term “expression cassette” refers to a fragment of DNA containing a foreign gene and having elements in addition to the foreign gene that allow for expression of that gene in a foreign host. Generally, an expression cassette will comprise the coding sequence of a selected gene and regulatory sequences preceding (5′ non-coding sequences) and following (3′ non-coding sequences) the coding sequence that are required for expression of the selected gene product. Thus, an expression cassette is typically composed of: 1) a promoter sequence; 2) a coding sequence [“ORF”]; and, 3) a 3′ untranslated region (i.e., a terminator) that, in eukaryotes, usually contains a polyadenylation site. The expression cassette(s) is usually included within a vector, to facilitate cloning and transformation. Different expression cassettes can be transformed into different organisms including bacteria, yeast, plants and mammalian cells, as long as the correct regulatory sequences are used for each host.

The terms “recombinant construct”, “expression construct”, “chimeric construct”, “construct”, and “recombinant DNA construct” are used interchangeably herein. A recombinant construct comprises an artificial combination of nucleic acid fragments, e.g., regulatory and coding sequences that are not found together in nature. For example, a recombinant construct may comprise one or more expression cassettes. In another example, a recombinant DNA construct may comprise regulatory sequences and coding sequences that are derived from different sources, or regulatory sequences and coding sequences derived from the same source, but arranged in a manner different than that found in nature. Such a construct may be used by itself or may be used in conjunction with a vector. If a vector is used, then the choice of vector is dependent upon the method that will be used to transform host cells as is well known to those skilled in the art. For example, a plasmid vector can be used. The skilled artisan is well aware of the genetic elements that must be present on the vector in order to successfully transform, select and propagate host cells comprising any of the isolated nucleic acid fragments described herein. The skilled artisan will also recognize that different independent transformation events will result in different levels and patterns of expression (Jones et al., EMBO J., 4:2411-2418 (1985); De Almeida et al., Mol. Gen. Genetics, 218:78-86 (1989)), and thus that multiple events must be screened in order to obtain strains displaying the desired expression level and pattern. Such screening may be accomplished by Southern analysis of DNA, Northern analysis of mRNA expression, Western and/or Elisa analyses of protein expression, formation of a specific product, phenotypic analysis or GC analysis of the PUFA products, among others.

The term “sequence analysis software” refers to any computer algorithm or software program that is useful for the analysis of nucleotide or amino acid sequences. “Sequence analysis software” may be commercially available or independently developed. Typical sequence analysis software will include, but is not limited to: 1) the GCG suite of programs (Wisconsin Package Version 9.0, Genetics Computer Group (GCG), Madison, Wis.); 2) BLASTP, BLASTN, BLASTX (Altschul et al., J. Mol. Biol., 215:403-410 (1990)); 3) DNASTAR (DNASTAR, Inc. Madison, Wis.); 4) Sequencher (Gene Codes Corporation, Ann Arbor, Mich.); and, 5) the FASTA program incorporating the Smith-Waterman algorithm (W. R. Pearson, Comput. Methods Genome Res., [Proc. Int. Symp.] (1994), Meeting Date 1992, 111-20. Editor(s): Suhai, Sandor. Plenum: New York, N.Y.). Within this description, whenever sequence analysis software is used for analysis, the analytical results are based on the “default values” of the program referenced, unless otherwise specified. As used herein “default values” will mean any set of values or parameters that originally load with the software when first initialized.

Standard recombinant DNA and molecular cloning techniques used herein are well known in the art and are described more fully in Sambrook, J., Fritsch, E. F. and Maniatis, T. Molecular Cloning: A Laboratory Manual; Cold Spring Harbor Laboratory Cold Spring Harbor, N.Y. (1989); by Silhavy, T. J., Bennan, M. L. and Enquist, L. W., Experiments with Gene Fusions, Cold Spring Harbor Laboratory: Cold Spring Harbor, N.Y. (1984); and by Ausubel, F. M. et al., Current Protocols in Molecular Biology, published by Greene Publishing Assoc. and Wiley-Interscience, Hoboken, N.J. (1987).

Esterases and lipases include those enzymes that catalyze the hydrolysis of ester bonds in water-insoluble, lipid substrates. Within Yarrowia lipolytica, a gene encoding a hypothetical protein weakly homologous to esterase/lipase has been identified (SEQ ID NO:1, “YALI0E19899g” locus, Dujon, B. et al., Nature, 430(6995):35-44 (2004)).

Yarrowia mutants having their native snf1 gene knocked-out can constitutively accumulate high levels of oil, even in nitrogenous growth media, when compared to the wild-type strains (U.S. Pat. Appl. Publ. No. 2010-0062502-A1). The snf1 gene encodes the alpha subunit of the SNF1 protein kinase, a heterotrimeric serine/threonine protein kinase that appears to function as a global regulator of gene expression. Particularly, SNF1 protein kinase regulates the transcription of numerous glucose-repressed genes, with a significant portion of those genes functioning in transcription and signal transduction. In general, when the heterotrimeric kinase is activated by phosphorylation, for example, in response to glucose limitation, ATP-producing catabolic pathways increase.

Based on microarray analysis in Y. lipolytica, it has been determined that over 200 genes are differentially expressed by more than 1.3-fold in snf1 knock-out strains, when compared to their expression in control strains (U.S. Pat. Appl. Publ. No. 2010-0062502-A1, Example 11 therein). Interestingly, the transcription of EL1 in these snf1 knock-out strains was increased as much as 2.93 times that of the wildtype strains.

Based on the above, the EL1 gene was identified as a potential source of new and improved yeast promoters for metabolic engineering of yeast and for controlling heterologous genes in yeast. In order to understand the means by which EL1 expression is regulated in Yarrowia, the EL1 promoter was isolated and its functional structure was mechanistically analyzed.

In general, a promoter useful for controlling the expression of heterologous genes in yeast should preferably meet criteria with respect to strength, activities, pH tolerance and inducibility, as described in U.S. Pat. No. 7,259,255. Additionally, today's complex metabolic engineering utilized for construction of yeast having the capability to produce a variety of heterologous polypeptides in commercial quantities requires a suite of promoters that are regulatable under a variety of natural growth and induction conditions.

Thus, described herein are a suite of promoter regions of an EL1 Yarrowia gene, useful for driving expression of any suitable coding region of interest in a transformed yeast cell. More specifically, described herein is an isolated nucleic acid molecule comprising a promoter region of an EL1 Yarrowia gene, wherein said promoter region of an EL1 Yarrowia gene is set forth in SEQ ID NO:6 (corresponding to the 5′ upstream −857 to −1 region of SEQ ID NO:1), and wherein said promoter optionally comprises at least one modification selected from the group consisting of:

-   -   a) a deletion at the 5′-terminus of 1, 2, 3, 4, 5, 6, 7, 8, 9,         10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,         26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41,         42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57,         58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73,         74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89,         90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104,         105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117,         118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130,         131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143,         144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156,         157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169,         170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182,         183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195,         196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208,         209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221,         222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234,         235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247,         248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260,         261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273,         274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286,         287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299,         300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312,         313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325,         326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338,         339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351,         352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364,         365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377,         378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390,         391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403,         404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416,         417, 418, 419, 420, 421, 422, 423, 424, 425, 426, 427, 428, 429,         430, 431, 432, 433, 434, 435, 436, 437, 438, 439, 440, 441, 442,         443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453, 454, 455,         456, 457, 458, 459, 460, 461, 462, 463, 464, 465, 466, 467, 468,         469, 470, 471, 472, 473, 474, 475, 476, 477, 478, 479, 480, 481,         482, 483, 484, 485, 486, 487, 488, 489, 490, 491, 492, 493, 494,         495, 496, 497, 498, 499, 500, 501, 502, 503, 504, 505, 506, 507,         508, 509, 510, 511, 512, 513, 514, 515, 516, 517, 518, 519, 520,         521, 522, 523, 524, 525, 526, 527, 528, 529, 530, 531, 532, 533,         534, 535, 536, 537, 538, 539, 540, 541, 542, 543, 544, 545, 546,         547, 548, 549, 550, 551, 552, 553, 554, 555, 556, 557, 558, 559,         560, 561, 562, 563, 564, 565, 566, 567, 568, 569, 570, 571, 572,         573, 574, 575, 576, 577, 578, 579, 580, 581, 582, 583, 584, 585,         586, 587, 588, 589, 590, 591, 592, 593, 594, 595, or 596         consecutive nucleotides, wherein the first nucleotide deleted is         the guanine [‘G’] nucleotide at position 1 of SEQ ID NO:6;     -   b) substitution of an adenine [‘A’] nucleotide for the cytosine         [‘C’] nucleotide at position 856 of SEQ ID NO:6;     -   c) substitution of a thymine [‘T’] nucleotide or a guanine [‘G’]         nucleotide for the cytosine [‘C’] nucleotide at position 856 of         SEQ ID NO:6;     -   d) substitution of a cytosine [‘C’] nucleotide for the guanine         [‘G’] nucleotide at position 382 of SEQ ID NO:6     -   e) substitution of an adenine [‘A’] nucleotide or a thymine         [‘T’] nucleotide for the guanine [‘G’] nucleotide at position         382 of SEQ ID NO:6;     -   f) insertion of a nucleotide sequence ‘TAAA’ between position         496 and position 497 of SEQ ID NO:6;     -   g) insertion of a nucleotides sequence ‘AC’ between position 596         and 597 of SEQ ID NO:6; and,     -   h) any combination of part a), part b), part c), part d), part         e), part f), and part g) above.         In some embodiments, the promoter region of an EL1 Yarrowia gene         is selected from the group consisting of SEQ ID NOs:2, 6, 8, 16,         21, 25, 27, and 29. These promoter regions are preferred to         provide relatively high levels of inducible promoter activity         when operably linked to a coding region of interest.

The relationship between the promoter regions of a Yarrowia EL1 gene selected from the group consisting of SEQ ID NOs:2, 6, 8, 21, 25, 16, 27, 29, and 30, supra, is readily observed upon alignment of the individual promoter sequences. Specifically, FIG. 2 (comprising FIGS. 2A, 2B, 2C, 2D, and 2E) provides an alignment of:

-   -   (a) the 1000 bp promoter region EL1F (SEQ ID NO:2);     -   (b) the 857 bp promoter region EL1L (SEQ ID NO:6);     -   (c) the 720 bp promoter region EL1LM-P2P1 (SEQ ID NO:21);     -   (d) the 718 bp promoter region EL1LM-P2P2 (SEQ ID NO:25);     -   (e) the 716 bp promoter region EL1LM-P2 (SEQ ID NO:16);     -   (f) the 361 bp promoter region EL1-P4 (SEQ ID NO:27);     -   (g) the 261 bp promoter region EL1-P5 (SEQ ID NO:29); and,     -   (h) the 207 bp promoter region EL1 minimal promoter (SEQ ID         NO:30);         Nucleotide differences are highlighted with a box and an arrow.

As will be obvious to one of skill in the art, the above discussion is by no means limiting to the description of suitable promoter regions of an EL1 Yarrowia gene. For example, alternate Yarrowia EL1 promoter regions may be longer than the 1000 bp sequence 5′ upstream of the nucleotide ‘A’ (designated as +1) of the translation initiation codon ‘ATG’ of SEQ ID NO:1, thereby encompassing additional nucleotides.

Similarly, it should be recognized that promoter fragments of various diminishing lengths may have identical promoter activity, since the exact boundaries of the regulatory sequences have not been completely defined. Thus, for example, it is also contemplated that a suitable promoter region of an EL1 Yarrowia gene could also include a promoter region of SEQ ID NO:6, wherein the 5′-terminus deletion was greater than 596 consecutive nucleotides.

More specifically, based on sequence analysis of the promoter region set forth in SEQ ID NO:29, and identification of six possible transcription initiator elements upstream of the ATG translation initiation codon, it is hypothesized herein that the minimal promoter region that could function for basal level transcription initiation of an operably linked coding region of interest encompasses (at least) the 207 bp 5′ upstream untranslated region from the ‘ATG’ translation initiation codon of an EL1 Yarrowia gene comprising the −255 to −48 region of SEQ ID NO:1; this 207 bp region is set forth independently as SEQ ID NO:30.

In alternate embodiments, SEQ ID NO:30 could be utilized as a minimal promoter to fuse with enhancers to drive expression of a coding region of interest. One of skill in the art would readily be able to conduct appropriate deletion studies to determine the appropriate length of a promoter region of an EL1 Yarrowia gene required to enable the desired level of promoter activity.

In alternate embodiments, SEQ ID NO:33 could be used as an enhancer to elevate levels of transcription from an adjacent eukaryotic coding region of interest, or fuse with a minimal promoter to form a recombinant promoter to drive expression of a coding region of interest. One of skill in the art would readily be able to conduct appropriate deletion studies to determine the minimal length of the enhancer region (SEQ ID NO:33) to enable the desired level of promoter activity.

Thus, in alternate embodiments, described herein is an isolated nucleic acid molecule comprising a promoter region of an EL1 Yarrowia gene, wherein said isolated nucleic acid molecule is selected from the group consisting of SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:16, SEQ ID NO:21, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:29, and SEQ ID NO:32.

More specifically, additional variant Yarrowia EL1 promoter regions may be constructed, wherein the DNA sequence of the promoter has one or more nucleotide substitutions (i.e., deletions, insertions, substitutions, or addition of one or more nucleotides in the sequence) which do not affect (in particular, impair) the yeast promoter activity. Regions that can be modified without significantly affecting the yeast promoter activity can be identified by deletion studies. A variant promoter of the present invention has at least about 10%, more preferably at least about 20%, more preferably at least about 40%, more preferably at least about 60%, more preferably at least about 80%, more preferably at least about 90%, more preferably at least about 100%, more preferably at least about 200%, more preferably at least about 300% and most preferably at least about 500% of the promoter activity of any of the Yarrowia EL1 promoter regions described herein as SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:16, SEQ ID NO:21, SEQ ID NO:25, SEQ ID NO:27, and SEQ ID NO:29.

U.S. Pat. No. 7,259,255 describes a variety of methods for mutagenesis suitable for the generation of mutant promoters. This would permit production of a putative promoter having, for example, a more desirable level of promoter activity in the host cell or a more desirable sequence for purposes of cloning (e.g., removal of a restriction enzyme site within the native promoter region). Similarly, the cited reference also discusses means to examine regions of a nucleotide of interest important for promoter activity (i.e., functional analysis via deletion mutagenesis to determine the minimum portion of the putative promoter necessary for activity).

All variant promoter regions of an EL1 Yarrowia gene, derived from the promoter regions described herein, are within the scope of the present disclosure.

Similarly, it should be noted that one could isolate regions upstream of the EL1 initiation codon in various Yarrowia species and strains, other than the region isolated herein from Yarrowia lipolytica ATCC #20362, and thereby identify alternate promoter regions of an EL1 Yarrowia gene. As is well known in the art, isolation of homologous promoter regions or genes using sequence-dependent protocols is readily possible using various techniques (see, U.S. Pat. No. 7,259,255). Examples of sequence-dependent protocols useful to isolate homologous promoter regions include, but are not limited to: 1) methods of nucleic acid hybridization; 2) methods of DNA and RNA amplification, as exemplified by various uses of nucleic acid amplification technologies [e.g., polymerase chain reaction [“PCR”], Mullis et al., U.S. Pat. No. 4,683,202; ligase chain reaction [“LCR”], Tabor, S. et al., Proc. Acad. Sci. U.S.A., 82:1074 (1985); or strand displacement amplification (SDA), Walker, et al., Proc. Natl. Acad. Sci. U.S.A., 89:392 (1992)]; 3) methods of library construction and screening by complementation; and, 4) methods of genome sequencing. Based on sequence conservation between related organisms, one would expect that the promoter regions would likely share significant homology (i.e., at least about 70-85% identity, more preferably at least about 85-90% identity and more preferably at least about 90-95% identity); however, one or more differences in nucleotide sequence could be observed when aligned with promoter regions of comparable length derived from the upstream region of SEQ ID NO:2. For example, one of skill in the art could readily isolate the Yarrowia EL1 promoter region from any of the various Y. lipolytica strains available through the American Type Culture Collection [“ATCC”], including, for example #8661, #8662, #9773, #15586, #16617, #16618, #18942, #18943, #18944, #18945, #20114, #20177, #20182, #20225, #20226, #20228, #20327, #20255, #20287, #20297, #20315, #20320, #20324, #20336, #20341, #20346, #20348, #20363, #20364, #20372, #20373, #20383, #20390, #20400, #20460, #20461, #20462, #20496, #20510, #20628, #20688, #20774, #20775, #20776, #20777, #20778, #20779, #20780, #20781, #20794, #20795, #20875, #20241, #20422, #20423, #32338, #32339, #32340, #32341, #34342, #32343, #32935, #34017, #34018, #34088, #34922, #34922, #38295, #42281, #44601, #46025, #46026, #46027, #46028, #46067, #46068, #46069, #46070, #46330, #46482, #46483, #46484, #46436, #60594, #62385, #64042, #74234, #76598, #76861, #76862, #76982, #90716, #90811, #90812, #90813, #90814, #90903, #90904, #90905, #96028, #201241, #201242, #201243, #201244, #201245, #201246, #201247, #201249, or #201847. Similarly, the following strains of Yarrowia lipolytica could be obtained from the Herman J. Phaff Yeast Culture Collection, University of California Davis (Davis, Calif.): Y. lipolytica 49-14, Y. lipolytica 49-49, Y. lipolytica 50-140, Y. lipolytica 50-46, Y. lipolytica 50-47, Y. lipolytica 51-30, Y. lipolytica 60-26, Y. lipolytica 70-17, Y. lipolytica 70-18, Y. lipolytica 70-19, Y. lipolytica 70-20, Y. lipolytica 74-78, Y. lipolytica 74-87, Y. lipolytica 74-88, Y. lipolytica 74-89, Y. lipolytica 76-72, Y. lipolytica 76-93, Y. lipolytica 77-12T and Y. lipolytica 77-17. Or, strains could be obtained from the Laboratoire de Microbiologie et Génétique Moléculaire of Dr. Jean-Marc Nicaud, INRA Centre de Grignon, France, including for example, Yarrowia lipolytica JMY798 (Mlí{hacek over (a)}ková, K. et al., Appl. Environ. Microbiol. 70(7):3918-24 (2004)), Y. lipolytica JMY399 (Barth, G., and C. Gaillardin. In, Nonconventional Yeasts In Biotechnology; Wolf, W. K., Ed.; Springer-Verlag: Berlin, Germany, 1996; pp 313-388) and Y. lipolytica JMY154 (Wang, H. J., et al., J. Bacteriol. 181(17):5140-8 (1999)).

In general, microbial expression systems and expression vectors containing regulatory sequences that direct high level expression of foreign proteins are well known to those skilled in the art. Any of these could be used to construct chimeric genes, which could then be introduced into appropriate microorganisms via transformation to provide high-level expression of the encoded enzymes.

Vectors (e.g., constructs, plasmids) and DNA expression cassettes useful for the transformation of suitable microbial host cells are well known in the art. The specific choice of sequences present in the construct is dependent upon the desired expression products, the nature of the host cell and the proposed means of separating transformed cells versus non-transformed cells. Typically, however, the vector contains at least one expression cassette, a selectable marker and sequences allowing autonomous replication or chromosomal integration. Suitable expression cassettes comprise a region 5′ of the gene that controls transcription (e.g., a promoter), the gene coding sequence, and a region 3′ of the DNA fragment that controls transcriptional termination, i.e., a terminator. It is most preferred when both control regions are derived from genes from the transformed yeast cell, although they need not be derived from genes native to the host.

Herein, transcriptional control regions (also initiation control regions or promoters) that are useful to drive expression of a coding gene of interest in the desired yeast cell are those promoter regions of an EL1 Yarrowia gene, as described supra. Once the promoter regions are identified and isolated, they may be operably linked to a coding region of interest to create a chimeric gene. The chimeric gene may then be expressed in a suitable expression vector in transformed yeast cells, particularly in the cells of oleaginous yeast (e.g., Yarrowia lipolytica).

Coding regions of interest to be expressed in transformed yeast cells may be either endogenous to the host or heterologous. Genes encoding proteins of commercial value are particularly suitable for expression. For example, suitable coding regions of interest may include (but are not limited to) those encoding viral, bacterial, fungal, plant, insect, or vertebrate coding regions of interest, including mammalian polypeptides. Further, these coding regions of interest may be, for example, structural proteins, signal transduction proteins, transcription factors, enzymes (e.g., oxidoreductases, transferases, hydrolyases, lyases, isomerases, ligases), or peptides. A non-limiting list includes genes encoding enzymes such as acyltransferases, aminopeptidases, amylases, carbohydrases, carboxypeptidases, catalases, cellulases, chitinases, cutinases, cyclodextrin glycosyltransferases, deoxyribonucleases, esterases, alpha-galactosidases, beta-glucanases, beta-galactosidases, glucoamylases, alpha-glucosidases, beta-glucosidases, invertases, laccases, lipases, mannosidases, mutanases, oxidases, pectinolytic enzymes, peroxidases, phospholipases, phosphatases, phytases, polyphenoloxidases, proteolytic enzymes, ribonucleases, transglutaminases or xylanases.

Thus, one aspect of the present disclosure provides a recombinant construct comprising a Yarrowia EL1 promoter region, as well as recombinant expression vectors comprising the recombinant construct. The EL1 promoter may also be comprised within a chimeric gene.

Also provided herein is a method for the expression of a coding region of interest in a transformed yeast cell comprising:

-   -   a) providing a transformed yeast cell having a recombinant         construct, wherein the recombinant construct comprises:         -   (1) a promoter region of an EL1 Yarrowia gene; and         -   (2) a coding region of interest which is expressible in the             yeast cell;     -   wherein the promoter region is operably linked to the coding         region of interest; and     -   b) growing the transformed yeast cell of step (a) under         conditions whereby the recombinant construct is expressed.         The polypeptide so produced by expression of the recombinant         construct may optionally be recovered from the culture.

In some embodiments herein, preferred coding regions of interest are those encoding enzymes involved in the production of microbial oils, including omega-6 and omega-3 fatty acids (i.e., omega-6 and omega-3 fatty acid biosynthetic pathway enzymes). Thus, preferred coding regions include those encoding desaturases (e.g., delta-8 desaturases, delta-5 desaturases, delta-17 desaturases, delta-12 desaturases, delta-4 desaturases, delta-6 desaturases, delta-15 desaturases and delta-9 desaturases) and elongases (e.g., C_(14/16) elongases, C_(16/18) elongases, C_(18/20) elongases, C_(20/22) elongases, delta-6 elongases and delta-9 elongases).

More specifically, the omega-3/omega-6 fatty acid biosynthetic pathway is illustrated in FIG. 3. All pathways require the initial conversion of oleic acid [18:1] to linoleic acid [“LA”; 18:2], the first of the omega-6 fatty acids, by a delta-12 desaturase. Then, using the “delta-9 elongase/delta-8 desaturase pathway” and LA as substrate, long-chain omega-6 fatty acids are formed as follows: 1) LA is converted to eicosadienoic acid [“EDA”; 20:2] bp a delta-9 elongase; 2) EDA is converted to dihomo-gamma-linolenic acid [“DGLA”; 20:3] bp a delta-8 desaturase; 3) DGLA is converted to arachidonic acid [“ARA”; 20:4] bp a delta-5 desaturase; 4) ARA is converted to docosatetraenoic acid [“DTA”; 22:4] bp a C_(20/22) elongase; and, 5) DTA is converted to docosapentaenoic acid [“DPAn-6”; 22:5] by a delta-4 desaturase. To clarify, “omega-6 fatty acids” are polyunsaturated fatty acids having the first unsaturated double bond six carbon atoms from the omega (methyl) end of the molecule and additionally having a total of two or more double bonds, with each subsequent unsaturation occurring 3 additional carbon atoms toward the carboxyl end of the molecule.

The “delta-9 elongase/delta-8 desaturase pathway” can also use alpha-linolenic acid [“ALA”; 18:3] as substrate to produce long-chain omega-3 fatty acids as follows: 1) LA is converted to ALA, the first of the omega-3 fatty acids, by a delta-15 desaturase; 2) ALA is converted to eicosatrienoic acid [“ETrA”; 20:3] bp a delta-9 elongase; 3) ETrA is converted to eicosatetraenoic acid [“ETA”; 20:4] bp a delta-8 desaturase; 4) ETA is converted to eicosapentaenoic acid [“EPA”; 20:5] bp a delta-5 desaturase; 5) EPA is converted to docosapentaenoic acid [“DPA”; 22:5] bp a C_(20/22) elongase; and, 6) DPA is converted to docosahexaenoic acid [“DHA”; 22:6] bp a delta-4 desaturase. Optionally, omega-6 fatty acids may be converted to omega-3 fatty acids. For example, ETA and EPA are produced from DGLA and ARA, respectively, by delta-17 desaturase activity. To clarify, “omega-3 fatty acids” are polyunsaturated fatty acids having the first unsaturated double bond three carbon atoms away from the omega end of the molecule and additionally having a total of three or more double bonds, with each subsequent unsaturation occurring 3 additional carbon atoms toward the carboxyl end of the molecule.

Alternate pathways for the biosynthesis of omega-3/omega-6 fatty acids utilize a delta-6 desaturase and C_(18/20) elongase, that is, the “delta-6 desaturase/delta-6 elongase pathway”. More specifically, LA and ALA may be converted to GLA and stearidonic acid [“STA”; 18:4], respectively, by a delta-6 desaturase; then, a C_(18/20) elongase converts GLA to DGLA and/or STA to ETA. Downstream PUFAs are subsequently formed as described above.

One of skill in the art will appreciate that the disclosure herein also provides a method for the production of an omega-3 fatty acid or omega-6 fatty acid comprising:

-   -   a) providing a transformed oleaginous yeast comprising a         recombinant construct, wherein the recombinant construct         comprises:         -   i) a promoter region of an EL1 Yarrowia gene; and         -   ii) a coding region encoding at least one omega-3 fatty acid             or omega-6 fatty acid biosynthetic pathway enzyme;     -   wherein the promoter region and the coding region are operably         linked; and     -   b) growing the transformed oleaginous yeast of step (a) under         conditions whereby the at least one omega-3 fatty acid or         omega-6 fatty acid biosynthetic pathway enzyme is expressed and         the omega-3 fatty acid or the omega-6 fatty acid is produced;         and     -   c) optionally recovering the omega-3 fatty acid or the omega-6         fatty acid.         The omega-3 fatty acid or the omega-6 fatty acid may be selected         from the group consisting of: LA, GLA, EDA, DGLA, ARA, DTA,         DPAn-6, ALA, STA, ETrA, ETA, EPA, DPAn-3 and DHA.

Once a DNA cassette (e.g., comprising a chimeric gene comprising a promoter region of an EL1 Yarrowia gene, ORF and terminator) suitable for expression in a yeast cell has been obtained, it is placed in a plasmid vector capable of autonomous replication in the yeast cell, or it is directly integrated into the genome of the yeast cell. Integration of expression cassettes can occur randomly within the yeast genome or can be targeted through the use of constructs containing regions of homology with the yeast genome sufficient to target recombination to a specific locus. All or some of the transcriptional and translational regulatory regions can be provided by the endogenous locus where constructs are targeted to an endogenous locus.

Where two or more genes are expressed from separate replicating vectors, it is desirable that each vector has a different means of selection and should lack homology to the other construct(s) to maintain stable expression and prevent reassortment of elements among constructs. Judicious choice of regulatory regions, selection means and method of propagation of the introduced construct(s) can be experimentally determined so that all introduced chimeric genes are expressed at the necessary levels to provide for synthesis of the desired products.

U.S. Pat. No. 7,259,255 describes means to increase expression of a particular coding region of interest.

Constructs comprising the chimeric gene(s) of interest may be introduced into a yeast cell by any standard technique. These techniques include transformation (e.g., lithium acetate transformation [Methods in Enzymology, 194:186-187 (1991)]), protoplast transformation, bolistic impact, electroporation, microinjection, or any other method that introduces the chimeric gene(s) of interest into the yeast cell.

For convenience, a yeast cell that has been manipulated by any method to take up a DNA sequence, for example, in an expression cassette, is referred to herein as “transformed”, “transformant” or “recombinant” (as these terms will be used interchangeably herein). The transformed yeast will have at least one copy of the expression construct and may have two or more, depending upon whether the expression cassette is integrated into the genome or is present on an extrachromosomal element having multiple copy numbers.

The transformed yeast cell can be identified by various selection techniques, as described in U.S. Pat. No. 7,238,482, U.S. Pat. No. 7,259,255 and U.S. Pat. No. 7,932,077.

Following transformation, substrates upon which the translated products of the chimeric genes act may be produced by the yeast either naturally or transgenically, or they may be provided exogenously.

Yeast cells for expression of the instant chimeric genes comprising a promoter region of an EL1 Yarrowia gene may include yeast that grow on a variety of feedstocks, including simple or complex carbohydrates, fatty acids, organic acids, oils, glycerol and alcohols, and/or hydrocarbons over a wide range of temperature and pH values. It is contemplated that because transcription, translation and the protein biosynthetic apparatus are highly conserved, any yeast will be a suitable host for expression of the present chimeric genes.

As previously noted, yeast do not form a specific taxonomic or phylogenetic grouping, but instead comprise a diverse assemblage of unicellular organisms that occur in the Ascomycotina and Basidiomycotina, most of which reproduce by budding (or fission) and derive energy via fermentation processes. Examples of some yeast genera include, but are not limited to: Agaricostilbum, Ambrosiozyma, Arthroascus, Arxula, Ashbya, Babjevia, Bensingtonia, Botryozyma, Brettanomyces, Bullera, Candida, Clavispora, Cryptococcus, Cystofilobasidium, Debaryomyces, Dekkera, Dipodascus, Endomyces, Endomycopsella, Erythrobasidium, Fellomyces, Filobasidium, Galactomyces, Geotrichum, Guilliermondella, Hansenula, Hanseniaspora, Kazachstania, Kloeckera, Kluyveromyces, Kockovaella, Kodamaea, Komagataella, Kondoa, Lachancea, Leucosporidium, Leucosporidiella, Lipomyces, Lodderomyces, Issatchenkia, Magnusiomyces, Mastigobasidium, Metschnikowia, Monosporella, Myxozyma, Nadsonia, Nematospora, Oosporidium, Pachysolen, Pichia, Phaffia, Pseudozyma, Reniforma, Rhodosporidium, Rhodotorula, Saccharomyces, Saccharomycodes, Saccharomycopsis, Saturnispora, Schizoblastosporion, Schizosaccharomyces, Sirobasidium, Smithiozyma, Sporobolomyces, Sporopachydermia, Starmerella, Sympodiomycopsis, Sympodiomyces, Torulaspora, Tremella, Trichosporon, Trichosporiella, Trigonopsis, Udeniomyces, Wickerhamomyces, Williopsis, Xanthophyllomyces, Yarrowia, Zygosaccharomyces, Zygotorulaspora, Zymoxenogloea and Zygozyma.

In preferred embodiments, the transformed yeast is an oleaginous yeast. These organisms are naturally capable of oil synthesis and accumulation, wherein the oil can comprise greater than about 25% of the dry cell weight, more preferably greater than about 30% of the dry cell weight, more preferably greater than about 40% of the dry cell weight, more preferably greater than about 50% of the dry cell weight, and most preferably greater than about 60% of the dry cell weight. Genera typically identified as oleaginous yeast include, but are not limited to: Yarrowia, Candida, Rhodotorula, Rhodosporidium, Cryptococcus, Trichosporon and Lipomyces. More specifically, illustrative oil-synthesizing yeasts include: Rhodosporidium toruloides, Lipomyces starkeyii, L. lipoferus, Candida revkaufi, C. pulcherrima, C. tropicalis, C. utilis, Trichosporon pullans, T. cutaneum, Rhodotorula glutinus, R. graminis, and Yarrowia lipolytica (formerly classified as Candida lipolytica). Alternately, oil biosynthesis may be genetically engineered such that the transformed yeast can produce more than 25% oil of the dry cell weight, and thereby be considered oleaginous.

Most preferred is the oleaginous yeast Yarrowia lipolytica. In a further embodiment, most preferred are the Y. lipolytica strains designated as ATCC #20362, ATCC #8862, ATCC #18944, ATCC #76982 and/or LGAM S(7)1 (Papanikolaou S., and Aggelis G., Bioresour. Technol., 82(1):43-9 (2002)). The Y. lipolytica strain designated as ATCC #20362 was the particular strain from which the EL1 Yarrowia gene and promoter regions encompassed within SEQ ID NO:2 were isolated.

Specific teachings applicable for transformation of oleaginous yeasts (i.e., Yarrowia lipolytica) via integration techniques based on linearized fragments of DNA include U.S. Pat. No. 4,880,741 and U.S. Pat. No. 5,071,764 and Chen, D. C. et al. (Appl. Microbiol. Biotechnol., 48(2):232-235 (1997)). Specific teachings applicable for expression of omega-3 fatty acid or omega-6 fatty acid biosynthetic pathway enzymes in the oleaginous yeast Y. lipolytica are described in U.S. Pat. No. 7,238,482, U.S. Pat. No. 7,550,286, U.S. Pat. No. 7,588,931, U.S. Pat. No. 7,932,077, U.S. Pat. Appl. Publ. No. 2009-0093543-A1, and U.S. Pat. Appl. Publ. No. 2010-0317072-A1, each incorporated herein by reference in their entirety.

The transformed yeast cell is grown under conditions that optimize expression of the chimeric gene(s). In general, media conditions may be optimized by modifying the type and amount of carbon source, the type and amount of nitrogen source, the carbon-to-nitrogen ratio, the amount of different mineral ions, the oxygen level, growth temperature, pH, length of the biomass production phase, length of the oil accumulation phase and the time and method of cell harvest. Microorganisms of interest, such as oleaginous yeast (e.g., Yarrowia lipolytica) are generally grown in a complex medium such as yeast extract-peptone-dextrose broth [“YPD”] or a defined minimal media that lacks a component necessary for growth and thereby forces selection of the desired expression cassettes (e.g., Yeast Nitrogen Base (DIFCO Laboratories, Detroit, Mich.)).

Fermentation media suitable for the transformed yeast described herein should contain a suitable carbon source. Suitable carbon sources may include, but are not limited to: monosaccharides, disaccharides, oligosaccharides, polysaccharides, sugar alcohols, mixtures from renewable feedstocks, alkanes, fatty acids, esters of fatty acids, glycerol, monoglycerides, diglycerides, triglycerides, phospholipids, various commercial sources of fatty acids, and one-carbon sources, such as are described in U.S. Pat. No. 7,259,255. Hence it is contemplated that the source of carbon utilized may encompass a wide variety of carbon-containing sources and will only be limited by the choice of the yeast species. Although all of the above mentioned carbon sources and mixtures thereof are expected to be suitable herein, preferred carbon sources are sugars (e.g., glucose, invert sucrose, sucrose, fructose and combinations thereof), glycerols, and/or fatty acids (see U.S. Pat. Appl. Publ. No. 2011-0059204 A1).

Nitrogen may be supplied from an inorganic (e.g., (NH₄)₂SO₄) or organic (e.g., urea or glutamate) source. In addition to appropriate carbon and nitrogen sources, the fermentation media must also contain suitable minerals, salts, cofactors, buffers, vitamins and other components known to those skilled in the art suitable for the growth of the transformed yeast (and optionally, promotion of the enzymatic pathways necessary for omega-3/omega-6 fatty acid production). Particular attention is given to several metal ions, such as Fe⁺², Cu⁺², Mn⁺², Co⁺², Zn⁺² and Mg⁺², that promote synthesis of lipids and PUFAs (Nakahara, T. et al., Ind. Appl. Single Cell Oils, D. J. Kyle and R. Colin, eds. pp 61-97 (1992)).

Preferred growth media for the methods and transformed yeast cells described herein are common commercially prepared media, such as Yeast Nitrogen Base (DIFCO Laboratories, Detroit, Mich.). Other defined or synthetic growth media may also be used and the appropriate medium for growth of the transformant host cells will be known by one skilled in the art of microbiology or fermentation science. A suitable pH range for the fermentation is typically between about pH 4.0 to pH 8.0, wherein pH 5.5 to pH 7.5 is preferred as the range for the initial growth conditions. The fermentation may be conducted under aerobic or anaerobic conditions, wherein microaerobic conditions are preferred.

Typically, accumulation of high levels of omega-3/omega-6 fatty acids in oleaginous yeast cells requires a two-stage process, since the metabolic state must be “balanced” between growth and synthesis/storage of fats. Thus, most preferably, a two-stage fermentation process is necessary for the production of omega-3/omega-6 fatty acids in oleaginous yeast (e.g., Yarrowia lipolytica). This approach is described in U.S. Pat. No. 7,238,482.

Host cells comprising a suitable coding region of interest operably linked to promoter regions of an EL1 Yarrowia gene may be cultured using methods known in the art. For example, the cell may be cultivated by shake flask cultivation or small-/large-scale fermentation in laboratory or industrial fermentors performed in a suitable medium and under conditions allowing expression of the coding region of interest. Similarly, where commercial production of a product that relies on the instant genetic chimera is desired, a variety of culture methodologies may be applied. For example, large-scale production of a specific gene product over-expressed from a recombinant host may be produced by a batch, fed-batch or continuous fermentation process (see U.S. Pat. No. 7,259,255).

EXAMPLES

The present invention is further described in the following Examples, which illustrate reductions to practice of the invention but do not completely define all of its possible variations.

General Methods

Standard recombinant DNA and molecular cloning techniques used in the Examples are well known in the art and are described by: 1) Sambrook, J., Fritsch, E. F. and Maniatis, T., Molecular Cloning: A Laboratory Manual; Cold Spring Harbor Laboratory: Cold Spring Harbor, N.Y. (1989) (Maniatis); 2) T. J. Silhavy, M. L. Bennan, and L. W. Enquist, Experiments with Gene Fusions; Cold Spring Harbor Laboratory: Cold Spring Harbor, N.Y. (1984); and 3) Ausubel, F. M. et al., Current Protocols in Molecular Biology, published by Greene Publishing Assoc. and Wiley-Interscience (1987).

Materials and methods suitable for the maintenance and growth of microbial cultures are well known in the art. Techniques suitable for use in the following examples may be found as set out in Manual of Methods for General Bacteriology (Phillipp Gerhardt, R. G. E. Murray, Ralph N. Costilow, Eugene W. Nester, Willis A. Wood, Noel R. Krieg and G. Briggs Phillips, Eds), American Society for Microbiology: Washington, D.C. (1994)); or by Thomas D. Brock in Biotechnology: A Textbook of Industrial Microbiology, 2^(nd) ed., Sinauer Associates: Sunderland, Mass. (1989). All reagents, restriction enzymes and materials used for the growth and maintenance of microbial cells were obtained from Aldrich Chemicals (Milwaukee, Wis.), DIFCO Laboratories (Detroit, Mich.), GIBCO/BRL (Gaithersburg, Md.), New England Biolabs (Ipswich, Mass.), or Sigma Chemical Company (St. Louis, Mo.), unless otherwise specified. E. coli strains were typically grown at 37° C. on Luria Bertani [“LB”] plates.

General molecular cloning was performed according to standard methods (Sambrook et al., supra). DNA sequence was generated on an ABI Automatic sequencer using dye terminator technology (U.S. Pat. No. 5,366,860; EP 272,007) using a combination of vector and insert-specific primers. Sequence editing was performed in Sequencher (Gene Codes Corporation, Ann Arbor, Mich.). All sequences represent coverage at least two times in both directions. Comparisons of genetic sequences were accomplished using DNASTAR software (DNASTAR Inc., Madison, Wis.).

The meaning of abbreviations is as follows: “sec” means second(s), “min” means minute(s), “h” means hour(s), “d” means day(s), “μL” means microliter(s), “mL” means milliliter(s), “L” means liter(s), “μM” means micromolar, “mM” means millimolar, “M” means molar, “mmol” means millimole(s), “μmole” mean micromole(s), “g” means gram(s), “μg” means microgram(s), “ng” means nanogram(s), “U” means unit(s), “bp” means base pair(s) and “kB” means kilobase(s).

Nomenclature for Expression Cassettes:

The structure of an expression cassette will be represented by a simple notation system of “X::Y::Z”, wherein X describes the promoter fragment, Y describes the gene fragment, and Z describes the terminator fragment, which are all operably linked to one another.

Transformation and Cultivation of Yarrowia lipolytica:

Y. lipolytica strains with ATCC Accession Nos. #20362, #76982 and #90812 were purchased from the American Type Culture Collection (Rockville, Md.). Y. lipolytica strains were typically grown at 28-30° C. Agar plates were prepared as required by addition of 20 g/L agar to the liquid media, according to standard methodology.

Example 1 Isolation of the 5′ Upstream Regions of the EL1 Gene from Yarrowia lipolytica

According to the DNA sequence of the Yarrowia EL1 locus (ORF “YALI0E19899g”, Dujon, B. et al., Nature, 430(6995):35-44 (2004), SEQ ID NO:1 herein), the 1 kB length sequence 5′ upstream of the nucleotide ‘A’ (designated as +1) of the translation initiation codon ‘ATG’ was assumed to encode the promoter region (designated herein as EL1F, SEQ ID NO:2).

In order to study the promoter region upstream of the EL1 gene, oligonucleotides Y1210 (SEQ ID NO:3) and Y1211 (SEQ ID NO:4) were designed as primers to amplify a 857 bp 5′ upstream fragment from the nucleotide ‘A’ of the translation initiation codon ‘ATG’ of the EL1 gene. A ClaI site was included at the 5′ portion of oligonucleotide Y1210 (SEQ ID NO:3). In order to incorporate a Yarrowia translation initiation site consensus sequence (i.e., ACCATGG, U.S. Pat. No. 7,125,672) around the start codon ‘ATG’, the adenine nucleotide [“A”] at position −2 of the EL1 gene was mutated to a cytosine [“C”] in oligonucleotide Y1211 (SEQ ID NO:4)

The 857 bp 5′ upstream fragment of the EL1 gene was amplified using Y. lipolytica strain ATCC #20362 genomic DNA as template and oligonucleotides YL1210 and YL1211 as primers. The PCR amplification was carried out in a 50 μl total volume comprising: PCR buffer (containing 10 mM KCl, 10 mM (NH₄)₂SO₄, 20 mM Tris-HCl (pH 8.75), 2 mM MgSO₄, 0.1% Triton X-100), 100 μg/mL BSA (final concentration), 200 μM each deoxyribonucleotide triphosphate, 10 pmole of each primer and 1 μl of Pfu DNA polymerase (Stratagene, San Diego, Calif.)). The thermocycler conditions were set for 35 cycles at 95° C. for 1 min, 56° C. for 30 sec, and 72° C. for 1 min, followed by a final extension at 72° C. for 10 min.

The PCR product comprising the 857 bp 5′ upstream fragment of the EL1 gene was purified using a Qiagen PCR purification kit, followed by gel electrophoresis in 1% (weight/volume) agarose. The product was then cloned into the pCR4TOPO vector (Invitrogen, San Diego, Calif.). The ligated DNA sample was used to transform E. coli DH5α cells individually, and transformants were selected on LB agar containing ampicillin (100 μg/mL).

Analyses of the plasmid DNA from transformants confirmed the presence of an 857 bp fragment. The plasmid containing the 857 bp DNA fragment was designated pT-EL1 (SEQ ID NO:5). Sequence analyses showed that pT-EL1 contained a fragment of 857 bp (designated as EL1L, wherein the “L” is for “long”; SEQ ID NO:6) 5′ upstream sequence of the EL1 gene, with one nucleotide change at position −2 (“A” to “C”) as designed. The fragment was flanked by PmeI (from the vector) and NcoI restriction enzyme sites.

Example 2 Modifications to EL1L Synthesis of Promoter 857 bp EL1LM

The present Example describes the synthesis of pT-EL1-(S) and pT-EL1-(S)P2 plasmids, each comprising a modified EL1L promoter based on removal or insertion of a specific restriction enzyme site, respectively.

Specifically, plasmid pT-EL1-(S) (SEQ ID NO:7) was generated by site-directed mutagenesis using plasmid pT-EL1 (Example 1) as template, and oligonucleotides Y1212 (SEQ ID NO:9) and Y1213 (SEQ ID NO:10) as primers. The internal SphI site (i.e., ‘GCATGC’ at nucleotides 421 to 426 of SEQ ID NO:6) of the EL1L promoter was mutated into ‘GGATCC’ in plasmid pT-EL1-(S) (SEQ ID NO:7). The modified EL1L promoter lacking the internal SphI site within plasmid pT-EL1 was designated as 857 bp EL1LM (wherein the “LM” is for “long, modified”; SEQ ID NO:8).

Plasmid pT-EL1-(S)P2 (SEQ ID NO:11) was generated by site-directed mutagenesis using plasmid pT-EL1-(S) as template, and oligonucleotides Y1242 (SEQ ID NO:12) and Y1243 (SEQ ID NO:13) as primers. Specifically, an internal PmeI site was inserted into the EL1LM promoter at position −593 in pT-EL1-(S)P2 (SEQ ID NO:11). The modified EL1LM promoter comprising the new PmeI site within plasmid pT-EL1-(S)P2 was designated as 861 bp EL1LM+Pme (SEQ ID NO:31).

Example 3 Synthesis and Transformation of an Expression Plasmid Comprising 857 bp EL1LM Promoter

To perform comparative studies investigating the promoter activity of the 857 bp EL1LM promoter, an expression plasmid was created such that the EL1LM promoter was operably linked to a reporter gene (i.e., the E. coli gene encoding β-glucuronidase (“GUS”; Jefferson, R. A., Nature, 342(6251):837-838 (1989)).

U.S. Pat. No. 7,202,356 describes the synthesis of pDMW212 (FIG. 4A and SEQ ID NO:14 herein), comprising a recombinant FBA::GUS::XPR2 construct. More specifically, this expression cassette comprises an FBA promoter fragment (i.e., 5′ upstream untranslated region in front of the ‘ATG’ translation initiation codon of a fructose-bisphosphate aldolase enzyme [E.C. 4.1.2.13] encoded by the fba1 gene and that is necessary for expression), a GUS reporter gene fragment and an XPR2 terminator fragment (comprising ˜100 bp of the 3′ region of the Yarrowia Xpr gene (GenBank Accession No. M17741)), which are all operably linked to one another.

The PmeI/NcoI fragment of pDMW212 (comprising the FBA promoter within the chimeric FBA::GUS::XPR2 gene) was replaced with the 857 bp EL1LM promoter. Specifically, the PmeI/NcoI fragment of pT-EL1-(S) (Example 2), comprising the 857 bp EL1LM promoter, was ligated with the PmeI/NcoI linearized pDMW212 fragment, thereby creating plasmid pEL1GUS (FIG. 4B; SEQ ID NO:15) comprising a chimeric EL1LM::GUS::XPR2 gene. Thus, pEL1GUS contains the following components:

TABLE 3 Description of Plasmid pEL1GUS RE Sites and Nucleotide position in SEQ ID NO: 15 Description of Fragment aChimeric Gene Components ClaI/SacI 857 bp EL1LM::GUS::XPR, comprising: (8536-2023) 857 bp EL1LM promoter: 857 bp Y. lipolytica EL1LM promoter (SEQ ID NO: 8); GUS: E. coli beta-D-glucuronidase (GenBank Accession No. AAA68923); XPR2: ~100 bp of the 3′ region of Xpr gene of Y. lipolytica (GenBank Accession No. M17741) 3163-2283 ColE1 plasmid origin of replication 4093-3233 Ampicillin-resistance gene (Amp^(R)) for selection in E. coli EcoRI/SphI ARS18: Y. lipolytica centromere and autonomously (4923-6269) replication sequence 18 (GenBank Accession No. M91600) PmeI/SphI Leu2: beta-isopropylmalate dehydrogenase gene (8514-6269) of Y. lipolytica (GenBank Accession No. M37309)

Y. lipolytica strain Y4001 has been described in U.S. Pat. No. 7,709,239 (Example 3 therein). Strain Y4001, derived from Y. lipolytica ATCC #20362, was capable of producing about 17% eicosadienoic acid [“EDA”; 20:2 omega-6] relative to the total lipids. The final genotype of strain Y4001 with respect to wild type Y. lipolytica ATCC #20362 was: Leu-, GPD::FmD12::Pex20, EXP1::EgD9e::Lip1, FBAINm::EgD9eS::Lip2 and YAT1::ME3S::Pex16. Abbreviations are as follows: FmD12 is a Fusarium moniliforme delta-12 desaturase gene [U.S. Pat. No. 7,504,259]; MESS is a codon-optimized C_(16/18) elongase gene, derived from Mortierella alpina [U.S. Pat. No. 7,470,532]; EgD9e is a Euglena gracilis delta-9 elongase gene [U.S. Pat. No. 7,645,604]; and, EgD9eS is a codon-optimized delta-9 elongase gene, derived from E. gracilis [U.S. Pat. No. 7,645,604].

Plasmids pEL1GUS and pDMW212 were transformed separately into Y. lipolytica strain Y4001 according to the method of Chen, D. C. et al. (Appl. Microbiol Biotechnol., 48(2):232-235 (1997)) and as described in U.S. Pat. No. 7,709,239.

Transformed cells were plated onto Minimal Media [“MM”] plates lacking leucine and maintained at 30° C. for 2 to 3 days (MM comprises per liter: 20 g glucose, 1.7 g yeast nitrogen base without amino acids, 1.0 g proline, and pH 6.1 (do not need to adjust)). Thus, transformants were obtained comprising pEL1GUS and pDMW212 plasmids, respectively.

Example 4 Comparative Analyses of 857 bp EL1LM and FBA Promoter Activities in Yarrowia lipolytica Strain Y4001

The promoter activities of the 857 bp EL1LM promoter (SEQ ID NO:8) and FBA promoter were determined in Yarrowia transformants containing plasmids pEL1GUS and pDMW212, respectively, based on expression of the GUS reporter gene as measured by histochemical assays (Jefferson, R. A., Plant Mol. Biol. Reporter, 5:387-405 (1987)).

Specifically, Y. lipolytica transformants containing plasmids pEL1GUS and pDMW212 were grown from single colonies in 3 mL MM at 30° C. for 2 days. Then, 1 mL of cells was collected by centrifugation. The remaining cultures were centrifuged and washed 2 times with High Glucose Media [“HGM”], resuspended in 3 mL each of HGM and allowed to grow at 30° C. for another 5 days (HGM comprises per liter: 80 g glucose, 2.58 g KH₂PO₄ and 5.36 g K₂HPO₄, pH 7.5 (do not need to adjust)). Cell samples from cultures grown 2 days in MM, as well as cultures grown 2 days in MM and 5 days in HGM were collected by centrifugation, resuspended in 100 μl of histochemical staining buffer, and incubated at 30° C. Staining buffer was prepared by dissolving 5 mg of 5-bromo-4-chloro-3-indolyl glucuronide [“X-Gluc”] in 50 μl dimethyl formamide, followed by the addition of 5 mL 50 mM NaPO₄, pH 7.0.

The results (FIG. 5) of histochemical staining showed that the 857 bp EL1LM promoter in construct pEL1GUS was weakly active when the transformed Yarrowia cells were grown in MM media. By contrast, very strong expression was observed in identical Yarrowia strains growing in nitrogen-limited HGM media. As expected, the FBA promoter in construct pDMW212 demonstrated strong constitutive activity when pDMW212-transformed cells were grown in either MM or nitrogen-limited HGM media.

Based on the above results, one of skill in the art will therefore recognize that the EL1LM promoter set forth as SEQ ID NO:8 is a strong inducible promoter useful for expression of heterologous genes in transformed yeast, including Yarrowia. It is to be noted that truncated promoters derived from the EL1LM promoter set forth as SEQ ID NO:8 will comprise an adenine [‘A’] to cytosine [‘C’] substitution at position 856, which corresponds to position −1 in SEQ ID NO:1 (i.e., when the position corresponding to the ‘A’ nucleotide of the ‘ATG’ translation initiation site of the EL1 gene is considered +1), when compared to the wildtype 5′ upstream sequence. One of skill in the art will appreciate that a suitable promoter region of an EL1 Yarrowia gene may optionally comprise an adenine [‘A’] or a cytosine [‘C’] nucleotide at this position; alternately, a modified EL1 promoter may also tolerate substitution of a thymine [‘T’] nucleotide or guanine [‘G’] nucleotide for the wildtype adenine [‘A’]. It is also to be noted that SEQ ID NO:8, in comparison to SEQ ID NO:6, comprises a substitution of a cytosine [‘C’] nucleotide for a guanine [‘G’] nucleotide at position 382. Thus, modified EL1LM promoters may also tolerate substitution of an adenine [‘A’] nucleotide or thymine [‘T’] nucleotide for the wildtype guanine [‘G’] at this position.

Example 5 Synthesis and Transformation of Expression Plasmids pEL1GUS2, pEL1GUS2-P1, pEL1GUS2-P2, pEL1GUS2-P4 and pEL1GUS2-P5 Comprising 716 bp EL1LM-P2, 720 bp EL1LM-P2P1, 718 bp EL1LM-P2P2, 361 bp EL1-P4, and 261 bp EL1-P5 Promoters

Comparative studies were performed to investigate the promoter activity of modified EL1 promoters having lengths of 716 bp, 720 bp, 718 bp, 361 bp, or 261 bp. Expression plasmids pEL1GUS2, pEL1GUS2-P1, pEL1GUS2-P2, pEL1GUS2-P4 and pEL1GUS2-P5 were created, respectively, each comprising a modified EL1 promoter operably linked to the GUS reporter gene.

First, the PmeI/NcoI fragment of pDMW212 (comprising the FBA promoter within the chimeric FBA::GUS::XPR2 gene) was replaced with the 716 bp PmeI/NcoI fragment of pT-EL1-(S)P2 (designated EL1LM-P2, SEQ ID NO:16). Specifically, the PmeI/NcoI fragment of pT-EL1-(S)P2 (Example 2), comprising the 716 bp EL1LM-P2 promoter, was ligated with the PmeI/NcoI linearized pDMW212 fragment, thereby creating plasmid pEL1GUS2 (SEQ ID NO:17) comprising a chimeric 716 bp EL1LM-P2::GUS::XPR2 gene.

Second, site-directed mutagenesis was performed using pEL1GUS2 as template and oligonucleotides Y1254 (SEQ ID NO:18) and Y1255 (SEQ ID NO:19) as primers. Specifically, primer Y1254 was designed to insert four nucleotides (i.e., ‘TAAA’) at position 356 of SEQ ID NO:16, thereby resulting in creation of a PmeI site in the 716 bp EL1LM-P2 promoter in the resultant plasmid, pEL1GUS2-P1 (SEQ ID NO:20). The modified EL1LM-P2 promoter in pEL1GUS2-P1 was 720 bp in length and was designated as 720 bp EL1LM-P2P1 (SEQ ID NO:21).

Similarly, site-directed mutagenesis was performed using pEL1GUS2 as template and oligonucleotides Y1256 (SEQ ID NO:22), and Y1257 (SEQ ID NO:23) as primers. Primer Y1256 was designed to insert two nucleotides (i.e., ‘AC’) at position 456 of SEQ ID NO:16, thereby resulting in creation of a PmeI site in the 716 bp EL1LM-P2 promoter in the resultant plasmid, pEL1GUS2-P2 (SEQ ID NO:24). The modified EL1LM-P2 promoter in pEL1GUS2-P2 was 718 bp in length and was designated as 718 bp EL1LM-P2P2 (SEQ ID NO:25).

Next, pEL1GUS2-P1 was digested with PmeI and the large PmeI fragment was isolated and then self-ligated to generate plasmid pEL1GUS2-P4 (SEQ ID NO:26) comprising a chimeric EL1-P4::GUS::XPR2 gene, wherein the 361 bp fragment of SEQ ID NO:21 was designated 361 bp EL1-P4 (SEQ ID NO:27). Similarly, pEL1GUS2-P2 was digested with PmeI and the large PmeI fragment was isolated and then self-ligated to generate plasmid pEL1GUS2-P5 (SEQ ID NO:28) comprising a chimeric EL1-P5::GUS::XPR2 gene, wherein the 261 bp fragment of SEQ ID NO:25 was designated 261 bp EL1-P5 (SEQ ID NO:29).

Thus, pEL1GUS2 (SEQ ID NO:17), pEL1GUS2-P1 (SEQ ID NO:20), pEL1GUS2-P2 (SEQ ID NO:24), pEL1GUS2-P4 (SEQ ID NO:26) and pEL1GUS2-P5 (SEQ ID NO:28) are identical expression constructs, with the exception that either a 716 bp EL1LM-P2 (SEQ ID NO:16), 720 bp EL1LM-P2P1 (SEQ ID NO:21), 718 bp EL1LM-P2P2 (SEQ ID NO:25), 361 bp EL1-P4 (SEQ ID NO:27), or 261 bp EL1-P5 (SEQ ID NO:29) promoter derived from the 5′ upstream region of the Y. lipolytica EL1 gene was operably linked to the chimeric GUS::XPR2 gene.

Plasmids pEL1GUS, pEL1GUS2, pEL1GUS2-P1, pEL1GUS2-P2, pEL1GUS2-P4, and pEL1GUS2-P5 were transformed separately into Y. lipolytica strain Y4001 as described in Example 3. Transformant cells were plated onto MM plates lacking leucine and maintained at 30° C. for 2 to 3 days. Thus, transformants were obtained comprising the pEL1GUS, pEL1GUS2, pEL1GUS2-P1, pEL1GUS2-P2, pEL1GUS2-P4, and pEL1GUS2-P5 plasmids, respectively.

Example 6 Comparative Analysis of 857 bp EL1LM, 716 bp EL1LM-P2, 720 bp EL1LM-P2P1, 718 bp EL1LM-P2P2, 361 bp EL1-P4, and 261 bp EL1-P5 Promoter Activities in Yarrowia lipolytica Strain Y4001

The promoter activities of the 857 bp EL1LM (SEQ ID NO:8), 716 bp EL1LM-P2 (SEQ ID NO:16), 720 bp EL1LM-P2P1 (SEQ ID NO:21), 718 bp EL1LM-P2P2 (SEQ ID NO:25), 361 bp EL1-P4 (SEQ ID NO:27), and 261 bp EL1-P5 (SEQ ID NO:29) promoters were determined in Yarrowia transformants containing pEL1GUS, pEL1GUS2, pEL1GUS2-P1, pEL1GUS2-P2, pEL1GUS2-P4, and pEL1GUS2-P5, respectively. GUS activity in each expressed construct was measured by histochemical assays as described in Example 4.

The results of histochemical staining showed that the promoter activities of 716 bp EL1LM-P2 (SEQ ID NO:16), 720 bp EL1LM-P2P1 (SEQ ID NO:21), and 718 bp EL1LM-P2P2 (SEQ ID NO:25) were equivalent to the 857 bp EL1LM (SEQ ID NO:8, Example 4). Specifically, each of the three promoters was weakly active when their respective transformed Yarrowia cells were grown in MM, but were very strongly active when their constructs were expressed by cells grown in nitrogen-limited HGM media. This indicated that the activity of the 716 bp EL1LM-P2 promoter (SEQ ID NO:16) was not affected by the 4 bp insertion at position −361 (EL1LM-P2P1, SEQ ID NO:21) or the 2 bp insertion at position −261 (EL1LM-P2P2, SEQ ID NO:25).

The results also showed that the 361 bp EL1-P4 promoter (SEQ ID NO:27) was weakly induced when cells expressing pEL1GUS2-P4 were grown in nitrogen-limited HGM media, which signaled the presence of an enhancer responsible for the induced activity of EL1LM and other modified promoters derived therefrom between positions 141 and 496 of EL1LM (SEQ ID NO:8) (corresponding to positions −716 and −361, respectively, in SEQ ID NO:1, where the ‘A’ of the ATG start codon is designated as +1). This enhancer is set forth herein as SEQ ID NO:33. The results further showed that the 261 bp EL1-P5 promoter (SEQ ID NO:29) was more strongly induced compared to the 361 bp EL1-P4 promoter (SEQ ID NO:27) when cells expressing pEL1GUS2-P5 were grown in nitrogen-limited HGM media, which indicated the presence of a silencer responsible for the reduced activity of the 361 bp EL1-P4 promoter (SEQ ID NO:27). This silencer is located between positions 496 and 596 of EL1LM (SEQ ID NO:8) (corresponding to positions −361 and −261, respectively, in SEQ ID NO:1, where the ‘A’ of the ATG start codon is designated as +1).

Based on the above results, one of skill in the art will recognize that the EL1LM promoter set forth as SEQ ID NO:8 can be truncated and retain promoter activity. Deleting the region defined by nucleotide positions 1 to 496 bp of SEQ ID NO:8 resulted in the active mutant promoter described herein as 361 bp EL1-P4, while deleting the region defined by nucleotide positions 1 to 596 bp of SEQ ID NO:8 resulted in the active mutant promoter described herein as 261 bp EL1-P5 (FIG. 1). It is therefore assumed that a variety of modified EL1LM promoters could be utilized for expression of a coding region of interest in a Yarrowia host cell, wherein the promoter optionally comprises at least one modification selected from the group consisting of: a deletion at the 5′-terminus of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431, 432, 433, 434, 435, 436, 437, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 460, 461, 462, 463, 464, 465, 466, 467, 468, 469, 470, 471, 472, 473, 474, 475, 476, 477, 478, 479, 480, 481, 482, 483, 484, 485, 486, 487, 488, 489, 490, 491, 492, 493, 494, 495, 496, 497, 498, 499, 500, 501, 502, 503, 504, 505, 506, 507, 508, 509, 510, 511, 512, 513, 514, 515, 516, 517, 518, 519, 520, 521, 522, 523, 524, 525, 526, 527, 528, 529, 530, 531, 532, 533, 534, 535, 536, 537, 538, 539, 540, 541, 542, 543, 544, 545, 546, 547, 548, 549, 550, 551, 552, 553, 554, 555, 556, 557, 558, 559, 560, 561, 562, 563, 564, 565, 566, 567, 568, 569, 570, 571, 572, 573, 574, 575, 576, 577, 578, 579, 580, 581, 582, 583, 584, 585, 586, 587, 588, 589, 590, 591, 592, 593, 594, 595, or 596 consecutive nucleotides, wherein the first nucleotide deleted is the guanine [‘G’] nucleotide at position 1 of SEQ ID NO:8. It is further assumed that SEQ ID NO:33 could be used as an enhancer to elevate levels of transcription of an operably linked eukaryotic promoter, thereby increasing transcription of an adjacent gene.

FIGS. 2A, 2B, 2C, 2D, and 2E is an alignment of the following Y. lipolytica EL1 promoter regions described herein: the EL1F (SEQ ID NO:2) promoter region, which is the 1000 bp 5′ upstream sequence (i.e., the −1000 to −1 region) of the EL1 gene in Yarrowia lipolytica, wherein the nucleotide ‘A’ of the EL1 translation initiation codon ‘ATG’ was designated as +1; the 716 bp EL1LM-P2 (SEQ ID NO:16) promoter region; the 720 bp EL1LM-P2P1 (SEQ ID NO:21) promoter region; the 718 bp EL1LM-P2P2 (SEQ ID NO:25) promoter region; the 361 bp EL1-P4 (SEQ ID NO:27) promoter region; and the 261 bp EL1-P5 (SEQ ID NO:29) promoter region. Sequence differences are noted with an arrow over the alignment and a box.

All of the modified promoters derived from the EL1F promoter set forth as SEQ ID NO:2 (i.e., 857 bp EL1L, 857 bp EL1LM, 716 bp EL1LM-P2, 720 bp EL1LM-P2P1, 718 bp EL1LM-P2P2, 361 bp EL1-P4, and 261 bp EL1-P5) comprise an adenine [‘A’] to cytosine [‘C’] substitution at the nucleotide corresponding to position −2 in SEQ ID NO:1. One of skill in the art will appreciate that a suitable promoter region of an EL1 Yarrowia gene may optionally comprise an adenine [‘A’] or a cytosine [‘C’] nucleotide at position −2; alternately, the modified EL1 promoter may also tolerate substitution of a thymine [‘T’] nucleotide or guanine [‘G’] nucleotide for the wildtype adenine [‘A’] at position −2.

Additionally, it is to be noted that, compared to SEQ ID NO:6, SEQ ID NO:8 comprises a substitution of a cytosine [‘C’] nucleotide for a guanine [‘G’] nucleotide at position 382; thus modified EL1 promoters may also tolerate substitution of a thymine [‘T’] nucleotide or an adenine [‘A’] nucleotide for the wildtype guanine [‘G’] at this position.

Example 7 Sequence Analysis of Promoter Regions of an EL1 Yarrowia Gene

The present Example describes the lack of a TATA-box within promoter regions of the EL1 Yarrowia gene.

Although promoters interact with the TATA binding protein [“TBP”] to create a transcription initiation complex from which RNA polymerase II transcribes the DNA coding sequence, only some promoters contain a TATA box to which TBP binds directly while other promoters are TATA-less promoters. The “TATA box” or “Goldberg-Hogness box” is a DNA sequence (i.e., cis-regulatory element) found in the promoter region of some genes in archaea and eukaryotes. For example, approximately 24% of human genes contain a TATA box within the core promoter (Yang C, et al., Gene, 389:52-65 (2007)); phylogenetic analysis of six Saccharomyces species revealed that about 20% of the 5,700 yeast genes contained a TATA-box element (Basehoar et al., Cell, 116:699-709 (2004)). The TATA box has a core DNA sequence of 5′-TATAAA-3′ or a variant thereof and is usually located ˜200 to 25 base pairs upstream of the transcriptional start site. The transcription initiation complex forms at the site of the TATA box (Smale and Kadonaga, T., Ann. Rev. Biochem. 72:449-479 (2003)). This complex comprises the TATA binding protein, RNA polymerase II, and various transcription factors (i.e., TFIID, TFIIA, TFIIB, TFIIF, TFIIE and TFIIH). Both the TATA box itself and the distance between the TATA box and transcription start site affect activity of TATA box-containing promoters in eukaryotes (Zhu et al., Plant Cell, 7:1681-1689 (1995)).

The genes within Yarrowia can be largely classified into three classes according to their promoter sequences. Specifically, the first class of genes includes those comprising a TATA box, usually, ˜130 to 20 base pairs upstream of the gene's transcription start site. The second class of genes includes those comprising an initiator element(s) around the gene's transcription start site. And, the third class of genes lacks both a TATA box and initiator element in the gene's promoter region.

Analysis of the sequence of the 261 bp EL1-P5 promoter region (Examples 5 and 6; SEQ ID NO:29) revealed that the promoter region does not contain a typical TATA-box. However, six possible initiator elements (PyA+1(T/A)Pu, Zhang et al., Nucleic Acids Res. 33:2838-2851 (2005) were identified within a 207 bp sequence of the EL1-P5 promoter region (corresponding to nucleotides 6 to 213 of SEQ ID NO:29, which is equivalent to the −255 to −48 region upstream of the ‘ATG’ translation initiation codon of the EL1 gene). Based on identification of this 207 bp fragment, it is believed that a suitable minimal EL1 promoter region for basal level and some induced transcription initiation would comprise this fragment, set forth herein as SEQ ID NO:30. It is also hypothesized that the 255 base pair sequence (i.e., set forth as SEQ ID NO:32) spanning the −255 to −1 region upstream of the ‘ATG’ translation initiation codon of the EL1 gene would be suitable for basal level transcription initiation.

Example 8 Comparison of Various Yarrowia EL1 Promoter Regions

The present Example summarizes the relative activity of various EL1 promoter regions exemplified in Examples 1-6 above. It was concluded that the EL1 promoter is a very strong inducible promoter that can effectively be used to drive high level expression of various genes in engineered Yarrowia strains under nitrogen-limited conditions, as shown in Table 54 below.

TABLE 4 Summary of Relative Activity of Various EL1 Promoter Regions Construct Promoter Operably Promoter Activity Comprising GUS Linked to GUS Cultured Cultured in Reporter Reporter Promoter Length in MM* MM + HGM** pEL1GUS EL1LM 857 bp + +++ (SEQ ID NO: 15) (SEQ ID NO: 8) pEL1GUS2 EL1LM-P2 716 bp + +++ (SEQ ID NO: 17) (SEQ ID NO: 16) pEL1GUS2-P1 EL1LM-P2P1 720 bp + +++ (SEQ ID NO: 20) (SEQ ID NO: 21) pEL1GUS2-P2 EL1LM-P2P2 718 bp + +++ (SEQ ID NO: 24) (SEQ ID NO: 25) pEL1GUS2-P4 EL1-P4 361 bp + + (SEQ ID NO: 26) (SEQ ID NO: 27) pEL1GUS2-P5 EL1-P5 261 bp + ++ (SEQ ID NO: 28) (SEQ ID NO: 29) *Cultured In MM refers to 2 days growth in MM. **Cultured in MM + HGM refers to 2 days growth in MM, followed by 3 days growth in HGM. 

1. A method for the expression of a coding region of interest in a transformed yeast cell comprising: a) providing a transformed yeast cell having a recombinant construct, wherein the recombinant construct comprises: (1) a promoter region of an EL1 Yarrowia gene; and (2) a coding region of interest which is expressible in the yeast cell; wherein the promoter region is operably linked to the coding region of interest; and b) growing the transformed yeast cell of step (a) under conditions whereby the recombinant construct of step (a) is expressed.
 2. The method according to claim 1, wherein the promoter region of the EL1 Yarrowia gene comprises a sequence selected from the group consisting of SEQ ID NO:30 and SEQ ID NO:32.
 3. The method according to claim 1, wherein the promoter region of the EL1 Yarrowia gene comprises SEQ ID NO:6, wherein said promoter region optionally comprises at least one modification selected from the group consisting of: a) a deletion at the 5′-terminus of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431, 432, 433, 434, 435, 436, 437, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 460, 461, 462, 463, 464, 465, 466, 467, 468, 469, 470, 471, 472, 473, 474, 475, 476, 477, 478, 479, 480, 481, 482, 483, 484, 485, 486, 487, 488, 489, 490, 491, 492, 493, 494, 495, 496, 497, 498, 499, 500, 501, 502, 503, 504, 505, 506, 507, 508, 509, 510, 511, 512, 513, 514, 515, 516, 517, 518, 519, 520, 521, 522, 523, 524, 525, 526, 527, 528, 529, 530, 531, 532, 533, 534, 535, 536, 537, 538, 539, 540, 541, 542, 543, 544, 545, 546, 547, 548, 549, 550, 551, 552, 553, 554, 555, 556, 557, 558, 559, 560, 561, 562, 563, 564, 565, 566, 567, 568, 569, 570, 571, 572, 573, 574, 575, 576, 577, 578, 579, 580, 581, 582, 583, 584, 585, 586, 587, 588, 589, 590, 591, 592, 593, 594, 595, or 596 consecutive nucleotides, wherein the first nucleotide deleted is the guanine [‘G’] nucleotide at position 1 of SEQ ID NO:6; b) substitution of an adenine [‘A’] nucleotide for the cytosine [‘C’] nucleotide at position 856 of SEQ ID NO:6; c) substitution of a thymine [‘T’] nucleotide or a guanine [‘G’] nucleotide for the cytosine [‘C’] nucleotide at position 856 of SEQ ID NO:6; d) substitution of a cytosine [‘C’] nucleotide for the guanine [‘G’] nucleotide at position 382 of SEQ ID NO:6; e) substitution of an adenine [‘A’] nucleotide or a thymine [‘T’] nucleotide for the guanine [‘G’] nucleotide at position 382 of SEQ ID NO:6; f) insertion of a nucleotide sequence ‘TAAA’ between position 496 and position 497 of SEQ ID NO:6; g) insertion of a nucleotide sequence ‘AC’ between position 596 and 597 of SEQ ID NO:6; and h) any combination of part a), part b), part c), part d), part e), part f), and part g).
 4. The method according to claim 3, wherein the promoter region of the EL1 Yarrowia gene comprises a sequence selected from the group consisting of SEQ ID NO:8, SEQ ID NO:16, SEQ ID NO:21, SEQ ID NO:25, SEQ ID NO:27 and SEQ ID NO:29.
 5. The method according to claim 4, wherein the promoter region of the EL1 Yarrowia gene comprises SEQ ID NO:29, and wherein said promoter region optionally comprises at least one modification selected from the group consisting of: a) a deletion at the 5′-terminus of 1, 2, 3, 4, 5, or 6 consecutive nucleotides, wherein the first nucleotide deleted is the thymine nucleotide [‘T’] at position 1 of SEQ ID NO:29; b) a deletion at the 3′-terminus of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, or 48 consecutive nucleotides, wherein the first nucleotide deleted is the cytosine [‘C’] at position 261 of SEQ ID NO:29; and c) a deletion of part (a) in combination with a substitution of a thymine [‘T’] nucleotide, an adenine [‘A’] nucleotide, or a guanine [‘G’] nucleotide for the cytosine [‘C’] nucleotide at position 260 of SEQ ID NO:29.
 6. The method according to claim 1, wherein the transformed yeast cell is an oleaginous yeast cell.
 7. The method of claim 6, wherein the oleaginous yeast cell is a member of a genus selected from the group consisting of Yarrowia, Candida, Rhodotorula, Rhodosporidium, Cryptococcus, Trichosporon and Lipomyces.
 8. The method according to claim 1, wherein the coding region of interest encodes a polypeptide, wherein the polypeptide is selected from the group consisting of: desaturases, elongases, acyltransferases, aminopeptidases, amylases, carbohydrases, carboxypeptidases, catalases, cellulases, chitinases, cutinases, cyclodextrin glycosyltransferases, deoxyribonucleases, esterases, alpha-galactosidases, beta-galactosidases, glucoamylases, alpha-glucosidases, beta-glucanases, beta-glucosidases, invertases, laccases, lipases, mannosidases, mutanases, oxidases, pectinolytic enzymes, peroxidases, phospholipases, phosphatases, phytases, polyphenoloxidases, proteolytic enzymes, ribonucleases, transglutaminases and xylanases.
 9. The method according to claim 1, wherein the promoter region of the EL1 Yarrowia gene further (i) comprises an enhancer region set forth in SEQ ID NO:33, or (ii) is operably linked to said enhancer region.
 10. The method according to claim 1, wherein the coding region encodes at least one omega-3 fatty acid or omega-6 fatty acid biosynthetic pathway enzyme, and wherein an omega-3 fatty acid or omega-6 fatty acid is produced in step b).
 11. The method according to claim 10, wherein the omega-3 fatty acid or omega-6 fatty acid biosynthetic pathway enzyme is selected from the group consisting of desaturases and elongases.
 12. An isolated nucleic acid molecule comprising a promoter region of an EL1 Yarrowia gene as set forth in SEQ ID NO:6, wherein said promoter region optionally comprises at least one modification selected from the group consisting of: a) a deletion at the 5′-terminus of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431, 432, 433, 434, 435, 436, 437, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 460, 461, 462, 463, 464, 465, 466, 467, 468, 469, 470, 471, 472, 473, 474, 475, 476, 477, 478, 479, 480, 481, 482, 483, 484, 485, 486, 487, 488, 489, 490, 491, 492, 493, 494, 495, 496, 497, 498, 499, 500, 501, 502, 503, 504, 505, 506, 507, 508, 509, 510, 511, 512, 513, 514, 515, 516, 517, 518, 519, 520, 521, 522, 523, 524, 525, 526, 527, 528, 529, 530, 531, 532, 533, 534, 535, 536, 537, 538, 539, 540, 541, 542, 543, 544, 545, 546, 547, 548, 549, 550, 551, 552, 553, 554, 555, 556, 557, 558, 559, 560, 561, 562, 563, 564, 565, 566, 567, 568, 569, 570, 571, 572, 573, 574, 575, 576, 577, 578, 579, 580, 581, 582, 583, 584, 585, 586, 587, 588, 589, 590, 591, 592, 593, 594, 595, or 596 consecutive nucleotides, wherein the first nucleotide deleted is the guanine [‘G’] nucleotide at position 1 of SEQ ID NO:6; b) substitution of an adenine [‘A’] nucleotide for the cytosine [‘C’] nucleotide at position 856 of SEQ ID NO:6; c) substitution of a thymine [‘T’] nucleotide or a guanine [‘G’] nucleotide for the cytosine [‘C’] nucleotide at position 856 of SEQ ID NO:6; d) substitution of a cytosine [‘C’] nucleotide for the guanine [‘G’] nucleotide at position 382 of SEQ ID NO:6; e) substitution of an adenine [‘A’] nucleotide or a thymine [‘T’] nucleotide for the guanine [‘G’] nucleotide at position 382 of SEQ ID NO:6; f) insertion of a nucleotide sequence ‘TAAA’ between position 496 and position 497 of SEQ ID NO:6; g) insertion of a nucleotide sequence ‘AC’ between position 596 and 597 of SEQ ID NO:6; and h) any combination of part a), part b), part c), part d), part e), part f), and part g).
 13. The isolated nucleic acid molecule of claim 12, wherein the promoter region comprises a sequence selected from the group consisting of SEQ ID NO:8, SEQ ID NO:16, SEQ ID NO:21, SEQ ID NO:25, SEQ ID NO:27 and SEQ ID NO:29.
 14. The isolated nucleic acid molecule of claim 12, wherein the promoter region of the EL1 Yarrowia gene further (i) comprises an enhancer region set forth in SEQ ID NO:33, or (ii) is operably linked to said enhancer region.
 15. An isolated nucleic acid molecule comprising a promoter region of a EL1 Yarrowia gene comprising SEQ ID NO:30 or SEQ ID NO:32. 